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ran_script.txt
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1001 cd ..
1002 head Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
1003 sed -i 's/ /_/g' Arab_thali.fa
1004 head Arab_thali.fa
1005 gawk 'BEGIN{line=0}{ if ($0 !~/^>/ && $0 ~/ +/ ) {gsub(/ +/, //); line++} print}END{print line" lines with white spaces treated" > "/dev/stderr"}' Arabidopsis_thaliana.TAIR10.fa > Arab_thali.fa
1006 sudo apt install gawt
1007 sudo apt install gawk
1008 gawk 'BEGIN{line=0}{ if ($0 !~/^>/ && $0 ~/ +/ ) {gsub(/ +/, //); line++} print}END{print line" lines with white spaces treated" > "/dev/stderr"}' Arabidopsis_thaliana.TAIR10.fa > Arab_thali.fa
1009 head Arab_thali.fa
1010 perl -i.bak -pe "s/\s+$/\n/;" Arab_thali.fa
1011 head Arab_thali.fa
1012 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed1.fa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa 2> wt-ABA-3_report.log
1013 cd Mirdeep_miRNA/
1014 head wt-ABA-3_collapsed1.fa
1015 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa 2> wt-ABA-3_report.log
1016 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa
1017 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none none
1018 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1019 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fasta Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1020 ls
1021 head wt-ABA-3_collapsed.fasta
1022 head wt-ABA-3_collapsed1.fasta
1023 sed -i 's/x/x /g' wt-ABA-3_collapsed1.fasta
1024 head wt-ABA-3_collapsed1.fasta
1025 cd ..
1026 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed1.fastaa Arabidopsis_thaliana.TAIR10.fasta Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1027 cd ..
1028 cd microRNA_data/
1029 sanity_check_genome.pl Arab_thali.fa
1030 remove_white_space_in_id.pl Arab_thali.fa
1031 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fasta Arab_thali.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1032 head Arab_thali.fa
1033 cd Documents/
1034 cd microRNA_data/
1035 ls -l
1036 cd ..
1037 ls -l
1038 perl -MCPAN -e shell
1039 sudo perl -MCPAN -e shell
1040 curl -L http://xrl.us/installperlnix | bash
1041 exit
1042 perl -v
1043 cpan App::cpanminus
1044 perl -MCPAN -e shell
1045 sudo perl -MCPAN -e shell
1046 sudo apt-get install libterm-readline-gnu-perlsudo apt-get install libterm-readline-gnu-perl
1047 sudo apt-get install libterm-readline-gnu-perl
1048 perl -MCPAN -e shell
1049 sudo perl -MCPAN -e shell
1050 celar
1051 clear
1052 whereis htseq-count
1053 ls
1054 whereis python
1055 whereis mirdeep2
1056 whereis htseq-count
1057 clear
1058 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1059 ls -l
1060 cd mirPRo.1.1.4/
1061 clear
1062 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1063 cd ..
1064 ls -l
1065 cd mirdeep2/
1066 clear
1067 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa 2> wt-ABA-3_report.log
1068 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa
1069 clear
1070 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1071 Error: Perl PDF::API2 package not found
1072 sudo cpan PDF::API2
1073 make_html.pl
1074 clear
1075 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1076 clear
1077 cd mirdeep2/
1078 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1079 cd ..
1080 clear
1081 ls -l
1082 cd mirPRo.1.1.4/
1083 clear
1084 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1085 samtools -version
1086 cd ..
1087 ls -l
1088 cd samtools-1.9/
1089 ls -l
1090 make
1091 pwd
1092 /home/siva/samtools-1.9
1093 export PATH=$PATH: /home/siva/samtools-1.9
1094 cd ..
1095 cd mirPRo.1.1.4/
1096 ls
1097 clear
1098 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1099 clear
1100 cd ..
1101 ls
1102 ls -l
1103 clear
1104 git clone https://github.com/jehandzlik/Manatee.git
1105 cd Manatee/
1106 ls -l
1107 ./config
1108 sudo ./config
1109 cpan
1110 sudo cpan
1111 Manatee -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -o /home/siva/Documents/microRNA_data/Manatee -index /home/siva/Documents/microRNA_data/bowtie_index/arabidopsis_genome -genome /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa -annotation /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf
1112 ls -l
1113 clear
1114 manatee -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -o /home/siva/Documents/microRNA_data/Manatee -index /home/siva/Documents/microRNA_data/bowtie_index/arabidopsis_genome -genome /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa -annotation /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf
1115 cd ..
1116 mkdir samtools
1117 ls -l
1118 cd samtools
1119 make
1120 cd ..
1121 cd samtools-1.9/
1122 make
1123 make install
1124 sudo make install
1125 cd ..
1126 cd Manatee/
1127 clear
1128 manatee -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -o /home/siva/Documents/microRNA_data/Manatee -index /home/siva/Documents/microRNA_data/bowtie_index/arabidopsis_genome -genome /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa -annotation /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf
1129 nano manatee
1130 pwd
1131 cpan App::cpanminus
1132 sudo cpan App::cpanminus
1133 ls -l
1134 chmod 755 unitas/
1135 cd unitas/
1136 clear
1137 ls -l
1138 unitas_1.7.0.pl -h
1139 perl unitas_1.7.0.pl
1140 cpan
1141 clear
1142 perl unitas_1.7.0.pl
1143 perl -v
1144 perl unitas_1.7.0.pl
1145 cpan
1146 sudo cpan
1147 perl unitas_1.7.0.pl
1148 sudo cpan
1149 perl unitas_1.7.0.pl
1150 ls -l
1151 cd mirdeep2/
1152 ls
1153 clear
1154 ls -l
1155 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa \
1156 Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf mature_T.fa none hairpin_T.fa
1157 cd ..
1158 cd Documents/
1159 clear
1160 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa \
1161 Arabidopsis_thaliana.TAIR10.dna.toplevel.fa \
1162 Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf \
1163 cd microRNA_data/
1164 clear
1165 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa \
1166 Arabidopsis_thaliana.TAIR10.dna.toplevel.fa \
1167 Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf \
1168 clear
1169 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1170 cd ..
1171 cd mirdeep2/
1172 ls
1173 perl install.pl
1174 install.pl
1175 perl install.pl
1176 cd ..
1177 cd Documents/microRNA_data/
1178 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1179 cd Documents/microRNA_data/
1180 clear
1181 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1182 cd ..
1183 tar xvvzf PDF-API2-0.73.tar.gz
1184 cd PDF-API2-0.73/
1185 whereis miRDeep2
1186 perl Makefile.PL INSTALL_BASE= /home/siva/mirdeep2/bin/miRDeep2.pl LIB= /home/siva/mirdeep2/bin/miRDeep2.pl/lib
1187 perl Makefile.PL INSTALL_BASE= /home/siva/mirdeep2/bin/miRDeep2.pl LIB= /home/siva/mirdeep2/lib
1188 perl Makefile.PL INSTALL_BASE= /home/siva/mirdeep2/ LIB= /home/siva/mirdeep2/lib
1189 cd ..
1190 cd PDF-API2-0.73/
1191 echo $PATH
1192 cd ..
1193 git clone https://github.com/BenLangmead/bowtie.git
1194 cd bowtie/
1195 echo $PATH
1196 bowtie -version
1197 whereis bowtie
1198 whereis mirdeep2
1199 cd ..
1200 whereis mirdeep2
1201 cd mirdeep2/
1202 echo $PATH
1203 echo $PATH &>PATH
1204 cd ..
1205 whereis Vienna
1206 cd ViennaRNA-2.4.16/
1207 echo $PATH
1208 pwd
1209 ls
1210 cd ..
1211 cd randfold_src/
1212 pwd
1213 cd ..
1214 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/bin' >> ~/.bashrc
1215 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/perls/perl-5.28.0/bin' >> ~/.bashrc
1216 echo 'export PATH=$PATH:/home/siva/anaconda3/bin' >> ~/.bashrc
1217 echo 'export PATH=$PATH:/home/siva/anaconda3/condabin' >> ~/.bashrc
1218 echo 'export PATH=$PATH:/home/siva/novocraft' >> ~/.bashrc
1219 echo 'export PATH=$PATH:/home/siva/mirPRo.1.1.4/bin' >> ~/.bashrc
1220 echo 'export PATH=$PATH:/usr/bin/htseq-count' >> ~/.bashrc
1221 echo 'export PATH=$PATH:/home/siva/mirdeep2/src' >> ~/.bashrc
1222 echo 'export PATH=$PATH:/home/siva/samtools-1.9' >> ~/.bashrc
1223 echo '/home/siva/ViennaRNA-2.4.16/bin' >> ~/.bashrc
1224 echo '/home/siva/randfold_src' >> ~/.bashrc
1225 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/bin' >> ~/.bashrc
1226 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/perls/perl-5.28.0/bin' >> ~/.bashrc
1227 echo 'export PATH=$PATH:/home/siva/anaconda3/bin' >> ~/.bashrc
1228 echo 'export PATH=$PATH:/home/siva/anaconda3/condabin' >> ~/.bashrc
1229 echo 'export PATH=$PATH:/home/siva/novocraft' >> ~/.bashrc
1230 echo 'export PATH=$PATH:/home/siva/mirPRo.1.1.4/bin' >> ~/.bashrc
1231 echo 'export PATH=$PATH:/usr/bin/htseq-count' >> ~/.bashrc
1232 echo 'export PATH=$PATH:/home/siva/mirdeep2/src' >> ~/.bashrc
1233 echo 'export PATH=$PATH:/home/siva/samtools-1.9' >> ~/.bashrc
1234 echo '/home/siva/ViennaRNA-2.4.16/bin' >> ~/.bashrc
1235 echo '/home/siva/randfold_src' >> ~/.bashrc
1236 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/bin' >> ~/.bashrc
1237 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/perls/perl-5.28.0/bin' >> ~/.bashrc
1238 echo 'export PATH=$PATH:/home/siva/anaconda3/bin' >> ~/.bashrc
1239 echo 'export PATH=$PATH:/home/siva/anaconda3/condabin' >> ~/.bashrc
1240 echo 'export PATH=$PATH:/home/siva/novocraft' >> ~/.bashrc
1241 echo 'export PATH=$PATH:/home/siva/mirPRo.1.1.4/bin' >> ~/.bashrc
1242 echo 'export PATH=$PATH:/usr/bin/htseq-count' >> ~/.bashrc
1243 echo 'export PATH=$PATH:/home/siva/mirdeep2/src' >> ~/.bashrc
1244 echo 'export PATH=$PATH:/home/siva/samtools-1.9' >> ~/.bashrc
1245 echo 'export PATH=$PATH:/home/siva/ViennaRNA-2.4.16/bin' >> ~/.bashrc
1246 echo 'export PATH=$PATH:/home/siva/randfold_src' >> ~/.bashrc
1247 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/bin' >> ~/.bashrc
1248 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/perls/perl-5.28.0/bin' >> ~/.bashrc
1249 echo 'export PATH=$PATH:/home/siva/anaconda3/bin' >> ~/.bashrc
1250 echo 'export PATH=$PATH:/home/siva/anaconda3/condabin' >> ~/.bashrc
1251 echo 'export PATH=$PATH:/home/siva/novocraft' >> ~/.bashrc
1252 echo 'export PATH=$PATH:/home/siva/mirPRo.1.1.4/bin' >> ~/.bashrc
1253 echo 'export PATH=$PATH:/usr/bin/htseq-count' >> ~/.bashrc
1254 echo 'export PATH=$PATH:/home/siva/mirdeep2/src' >> ~/.bashrc
1255 echo 'export PATH=$PATH:/home/siva/samtools-1.9' >> ~/.bashrc
1256 echo 'export PATH=$PATH:/home/siva/ViennaRNA-2.4.16/bin' >> ~/.bashrc
1257 echo 'export PATH=$PATH:/home/siva/randfold_src' >> ~/.bashrc
1258 bowtie
1259 RNAfold -h
1260 randfold
1261 make_html
1262 make_html.pl
1263 clear
1264 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/bin' >> ~/.bashrc
1265 echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/perls/perl-5.28.0/bin' >> ~/.bashrc
1266 echo 'export PATH=$PATH:/home/siva/anaconda3/bin' >> ~/.bashrc
1267 echo 'export PATH=$PATH:/home/siva/anaconda3/condabin' >> ~/.bashrc
1268 echo 'export PATH=$PATH:/home/siva/ViennaRNA-2.4.16/bin' >> ~/.bashrc
1269 echo 'export PATH=$PATH:/home/siva/randfold_src' >> ~/.bashrc
1270 cd mirdeep2/
1271 cd ..
1272 cd Documents/microRNA_data/
1273 ls -l
1274 clear
1275 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1276 cd ..
1277 cd..
1278 cd ..
1279 cd bowtie/
1280 pwd
1281 echo 'export PATH=$PATH:/home/siva/bowtie' >> ~/.bashrc
1282 clear
1283 cd Documents/microRNA_data/
1284 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1285 cd Documents/microRNA_data/
1286 clear
1287 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1288 whereis bowtie
1289 locate bowtie
1290 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1291 echo 'export PATH=$PATH:/home/siva/bowtie' >> ~/.bashrc
1292 exit
1293 cd Documents/microRNA_data/
1294 miRDeep2.pl Mirdeep_miRNA/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf none none none
1295 cd ..
1296 cd ViennaRNA-2.4.16/
1297 ls -l
1298 ./configure
1299 make
1300 clear
1301 pwd
1302 ls -l
1303 python -version
1304 python --version
1305 where is Python
1306 whereis Python
1307 $PATH Python
1308 nano bash.src
1309 nano bashrc.sh
1310 $PATH
1311 pwd
1312 ls -l
1313 conda install -c conda-forge mamba
1314 clear
1315 mamba create -c conda-forge -c bioconda -n snakemake snakemake
1316 conda activate snakemake
1317 snakemake --help
1318 snakemake --version
1319 exit
1320 clear
1321 cd Documents/microRNA_data/
1322 clear
1323 mapper.pl TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m /
1324 -p bowtie_index/arabidopsis_genome /
1325 -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa /
1326 -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf /
1327 -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1328 cd Mirdeep_miRNA/
1329 find_read_count.pl wt-ABA-3_collapsed.fasta
1330 cd ..
1331 whereis bowtie-build
1332 whereis mirdeep2
1333 cd ..
1334 cd mirdeep2/
1335 cd ..
1336 cd Documents/microRNA_data/
1337 clear
1338 mapper.pl TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1339 mapper.pl TRIMMED/wt-ABA-1.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-1_collapsed.fa -t Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-1.txt
1340 mapper.pl TRIMMED/wt-ABA-2.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-2_collapsed.fa -t Mirdeep_miRNA/wt-ABA-2_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-2.txt
1341 mapper.pl TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1342 mapper.pl TRIMMED/wt-Control-1.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-1_collapsed.fa -t Mirdeep_miRNA/wt-Control-1_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-Control-1.txt
1343 mapper.pl TRIMMED/wt-Control-2.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-2_collapsed.fa -t Mirdeep_miRNA/wt-Control-2_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-Control-2.txt
1344 mapper.pl TRIMMED/wt-Control-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-3_collapsed.fa -t Mirdeep_miRNA/wt-Control-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-Control-3.txt
1345 clear
1346 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-ABA-1_collapsed.fa -y now -d
1347 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-ABA-2_collapsed.fa -y now -d
1348 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-ABA-3_collapsed.fa -y now -d
1349 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-Control-1_collapsed.fa -y now -d
1350 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-Control-2_collapsed.fa -y now -d
1351 quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-Control-3_collapsed.fa -y now -d
1352 whereis samtools
1353 whereis bowtie
1354 clear
1355 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1356 cpan install PDF::API2
1357 sudo cpan install PDF::API2
1358 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1359 perldoc PDF::API2
1360 cd ..
1361 cd PDF-API2-0.73/
1362 perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1363 cd ..
1364 conda install -c bioconda perl-pdf-api2
1365 perldoc PDF::API2
1366 whereis PDF::API2
1367 locate PDF::API2
1368 nano bashrc.sh
1369 nano .bashrc
1370 cd Documents/microRNA_data/
1371 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1372 cd ...
1373 cd ..
1374 tar xvvzf PDF-API2-0.73.tar.gz
1375 cd PDF-API2-0.73/
1376 pwd
1377 perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1378 perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/ LIB=/home/siva/mirdeep2/lib/
1379 perl Makefile.PL INSTALL_BASE=/home/siva/ LIB=/home/siva/mirdeep2/lib/
1380 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/ LIB=/home/siva/mirdeep2/lib/
1381 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1382 perl -l Makefile.PL INSTALL_BASE=/home/siva/ LIB=/home/siva/mirdeep2/lib
1383 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/essentials/PDF-API2-XS-1.001 PREFIX=/home/siva/mirdeep2/lib LIB=/home/siva/mirdeep2/lib
1384 cd ..
1385 cd mirdeep2/
1386 cd /home/siva/mirdeep2/essentials/PDF-API2-XS-1.001
1387 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/essentials/PDF-API2-XS-1.001 PREFIX=/home/siva/mirdeep2/lib LIB=/home/siva/mirdeep2/lib
1388 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/essentials/PDF-API2-XS-1.001 LIB=/home/siva/mirdeep2/lib
1389 make
1390 make test
1391 make install
1392 cd ..
1393 touch install_successful
1394 nano bashrc
1395 nano bashrc.h
1396 ls -l
1397 nano .bashrc
1398 clear
1399 cd /home/siva/Documents/microRNA_data
1400 bowtie-build Arabidopsis_thaliana.TAIR10.dna.toplevel.fa ara_gen
1401 sudo apt install bowtie
1402 bowtie-build Arabidopsis_thaliana.TAIR10.dna.toplevel.fa ara_gen
1403 cd Documents/microRNA_data/
1404 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1405 cd /home/siva/mirdeep2
1406 perl install.pl
1407 cd ..
1408 perl -MCPAN -e 'install Bundle::Compress::Zlib'
1409 cd mirdeep2/
1410 perl install.pl
1411 cd ..
1412 conda install -c bioconda perl-memoize
1413 cd mirdeep2/
1414 perl install.pl
1415 cd ..
1416 % cpanm CHI::Memoize
1417 perl
1418 sudo cpan CHI::Memoize
1419 sudo cpan Bundle::Compress::Zlib
1420 cd mirdeep2/
1421 perl install.pl
1422 nano .bashrc
1423 cd ..
1424 nano .bashrc
1425 cd Documents/microRNA_data/
1426 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1427 cd Documents/microRNA_data/
1428 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf none none none 2> wt-ABA-1_report.log
1429 cd /home/siva/PDF-API2-0.73
1430 ls -l
1431 perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1432 perl -l Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1433 sudo perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2 LIB=/home/siva/mirdeep2/lib
1434 sudo perl Makefile.PL INSTALL_BASE=/home/siva/mirdeep2/lib/perl5/x86_64-linux/perl5/x86_64-linux/PDF/API2 LIB=/home/siva/mirdeep2/lib
1435 locate Version.pm
1436 cd ..
1437 cd Documents/microRNA_data/
1438 miRDeep2.pl Mirdeep_miRNA/wt-ABA-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-1_collapsed_vs_genome.arf -d none none none 2> wt-ABA-1_report.log
1439 cd mirPRo.1.1.4/
1440 fastq_quality_filter -h
1441 fastx_collapser -h
1442 novoindex
1443 novoalign
1444 randfold
1445 RNAfold -h
1446 htseq-count
1447 whereis htseq-count
1448 gcc -v
1449 g++ -v
1450 clear
1451 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1452 htseq-count
1453 samtools
1454 clear
1455 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a 'null' -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other 'null' -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1456 cd ..
1457 sudo apt-get install python-matplotlib
1458 python
1459 nano .bashrc
1460 cd mirPRo.1.1.4/
1461 bin/mirpro_feature_pro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -t /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf -o ./miRNA
1462 bin/mirpro_feature_pro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.bam -t /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf -o ./miRNA
1463 bin/mirpro_feature_pro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.sorted.out.bam -t /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf -o ./miRNA
1464 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./miRNA -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1465 cd mirdeep2/
1466 perl install.pl
1467 sudo cpan install PDF::API2
1468 perl -MCPAN -e shell
1469 git clone
1470 git clone https://github.com/rajewsky-lab/mirdeep2.git
1471 cd mirdeep2/
1472 perl install.pl
1473 cd ..
1474 cd Documents/microRNA_data/
1475 mapper.pl /TRIMMED/wt-ABA-1.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1476 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1477 cd Documents/microRNA_data/
1478 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1479 cd ..
1480 cd mirdeep2/
1481 perl install.pl
1482 cd Documents/microRNA_data/
1483 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1484 cd Documents/microRNA_data/
1485 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1486 cd ..
1487 cd mirdeep2/
1488 perl install.pl
1489 exit
1490 cd Documents/microRNA_data/
1491 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1492 mapper.pl /TRIMMED/wt-ABA-3.fastq -e -d -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1493 mapper.pl TRIMMED/wt-Control-2.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-2_collapsed.fa -t Mirdeep_miRNA/wt-Control-2_collapsed_vs_genome.arf -v
1494 mapper.pl TRIMMED/wt-ABA-3.fastq -e -d -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-ABA-3_collapsed.fa -t Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -v &> Mirdeep_log/mapper_wt-ABA-3.txt
1495 mapper.pl TRIMMED/wt-Control-1.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-1_collapsed.fa -t Mirdeep_miRNA/wt-Control-1_collapsed_vs_genome.arf -v
1496 mapper.pl TRIMMED/wt-Control-2.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-2_collapsed.fa -t Mirdeep_miRNA/wt-Control-2_collapsed_vs_genome.arf -v 2> Mirdeep_log/mapper_wt-Control-2.txt
1497 mapper.pl TRIMMED/wt-Control-1.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-1_collapsed.fa -t Mirdeep_miRNA/wt-Control-1_collapsed_vs_genome.arf -v 2> Mirdeep_log/mapper_wt-Control-1.txt
1498 mapper.pl TRIMMED/wt-Control-3.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-3_collapsed.fa -t Mirdeep_miRNA/wt-Control-3_collapsed_vs_genome.arf -v 2> Mirdeep_log/mapper_wt-Control-3.txt
1499 mkdir Raw_microRNA_fastq_files
1500 mv *.fastq ./Raw_microRNA_fastq_files/
1501 ls -l
1502 bowtie-build Arabidopsis_thaliana.TAIR10.dna.toplevel.fa arabidopsis_genome
1503 mv *.ebwt /index
1504 mkdir index
1505 mv *.ebwt /index
1506 mv *.ebwt /index/
1507 ls -l
1508 mv *.ebwt index
1509 ls -l
1510 mkdir micro_RNA
1511 mv * micro_RNA/
1512 cp * micro_RNA/
1513 cp -r * micro_RNA/
1514 cd micr
1515 cd micro_RNA/
1516 ls -l
1517 rm -r micro_RNA/
1518 ls -l
1519 cd ..
1520 gunzip EMBOSS-6.6.0.tar.gz
1521 tar xvf EMBOSS-6.6.0.tar
1522 cd EMBOSS-6.6.0/
1523 ./configure
1524 make
1525 ~~exit
1526 exit
1527 cd Documents/microRNA_data/
1528 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-3 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-3 &
1529 cd Documents/microRNA_data/
1530 pwd
1531 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-3 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-3 &
1532 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-3 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-3 &
1533 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-1 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-1 &
1534 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-3 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-3 &
1535 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-3 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-3 &
1536 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-2 --bowtie_cores 2 --readfile TRIMMED/wt-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-2 &
1537 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-1 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-1 &
1538 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-3 --bowtie_cores 2 --readfile TRIMMED/wt-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-3 &
1539 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-1 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-1 &
1540 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-2 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-2 &
1541 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-1 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-1 &
1542 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-1 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-1 &
1543 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-2 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-2 &
1544 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-3 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-3 &
1545 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-2 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-2 &
1546 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-2 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-2 &
1547 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-1 --bowtie_cores 2 --readfile TRIMMED/wt-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-1 &
1548 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-2 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-2 &
1549 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-2 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-2 &
1550 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-1 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-1 &
1551 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-3 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-3 &
1552 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-1 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-1 &
1553 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-3 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-3 &
1554 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-2 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-2 &
1555 ls -l
1556 cd Documents/
1557 ls -l
1558 cd microRNA_data/
1559 ls -l
1560 cd ShortStack-Results/
1561 ls -l
1562 nano log_wt-ABA-3
1563 nano log_wt-ABA-2
1564 nano log_wt-ABA-1
1565 nano log_wt-Control-1
1566 nano log_wt-Control-3
1567 cd wt-Control-1
1568 ls -l
1569 nano Counts.txt
1570 nano ErrorLogs.txt
1571 nano Results.txt
1572 nano Unplaced.txt
1573 cd MIRNAs/
1574 ls -l
1575 cd ..
1576 rm -all
1577 rm -r *
1578 cd .local/share/Trash/
1579 rm -rf ~/.local/share/Trash/*
1580 cd ~/.local
1581 cd share/
1582 ls -l
1583 cd Trash/
1584 ls -l
1585 cd expunged/
1586 ls -l
1587 cd 475349224/
1588 ls -l
1589 cd Lib/
1590 ls -l
1591 cd ./
1592 cd /
1593 ls
1594 cd /home/siva/Documents/microRNA_data
1595 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-3 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-3 &
1596 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-3 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-3 &
1597 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-1 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-1 &
1598 ohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-1 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-1 &
1599 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-1 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-1 &
1600 bin/miRDeep2.pl Mirdeep_results/wt-ABA-3_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_results/wt-ABA-3_collapsed_vs_genome.arf none none none -d 2> Mirdeep_results/wt-ABA-3_report.log
1601 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-1 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-1 &
1602 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-3 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-3 &
1603 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-3 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-3 &
1604 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-2 --bowtie_cores 2 --readfile TRIMMED/wt-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-2 &
1605 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-1 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-1 &
1606 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-3 --bowtie_cores 2 --readfile TRIMMED/wt-Control-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-3 &
1607 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-1 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-1 &
1608 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-Control-2 --bowtie_cores 2 --readfile TRIMMED/m3k17-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-Control-2 &
1609 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-1 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-1 &
1610 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-1 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-1 &
1611 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-Control-2 --bowtie_cores 2 --readfile TRIMMED/m3k18-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-Control-2 &
1612 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-3 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-3 &
1613 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-Control-2 --bowtie_cores 2 --readfile TRIMMED/abi1-Control-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-Control-2 &
1614 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-2 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-2 &
1615 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-Control-1 --bowtie_cores 2 --readfile TRIMMED/wt-Control-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-Control-1 &
1616 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-2 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-2 &
1617 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-2 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-2 &
1618 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k18-ABA-1 --bowtie_cores 2 --readfile TRIMMED/m3k18-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k18-ABA-1 &
1619 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-3 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-3 &
1620 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/wt-ABA-1 --bowtie_cores 2 --readfile TRIMMED/wt-ABA-1.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_wt-ABA-1 &
1621 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/abi1-ABA-3 --bowtie_cores 2 --readfile TRIMMED/abi1-ABA-3.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_abi1-ABA-3 &
1622 nohup ShortStack-master/ShortStack --outdir ShortStack-Results/m3k17-ABA-2 --bowtie_cores 2 --readfile TRIMMED/m3k17-ABA-2.fastq --genomefile Arabidopsis_thaliana_TAIR10_dna_toplevel.fa > ShortStack-Results/log_m3k17-ABA-2 &
1623 do-release upgrade
1624 sudo do-release-upgrade -d
1625 sudo apt-get install
1626 sudo apt-get upgrade
1627 sudo do-release-upgrade -d
1628 sudo apt-get upgrade
1629 sudo do-release-upgrade -d
1630 xkill
1631 sudo shutdown -r now
1632 python get_candidates.py
1633 python2.7 get_candidates.py
1634 python --version
1635 python2
1636 cd ..
1637 python2 get_candidates.py
1638 python --version
1639 which python
1640 sudo apt install python2
1641 python2 --version
1642 python2.7 get_candidates.py
1643 python2.7.17 get_candidates.py
1644 python2 get_candidates.py
1645 python3 --version
1646 python -V
1647 python -v
1648 update-alternatives --list python
1649 sudo update-alternatives --list python
1650 python2.7 get_candidates.py
1651 apt-get install bedtools
1652 sudo apt-get install bedtools
1653 sort -k1,1 -k2,2n miRNA_candidates_v2.bed > candidates.sorted_v2.bed
1654 bedtools merge -i candidates.sorted_v2.bed -d -1 -s -nms > overlapping_v2.txt
1655 pwd
1656 cd Documents/microRNA_data/
1657 python filter.py
1658 python get_fasta.py
1659 python2 get_fasta.py
1660 python format_candidates.py
1661 python2 format_candidates.py
1662 python mature.py
1663 python -V
1664 python mirna_expression.py
1665 python2 mirna_expression.py
1666 python mirna_annotation.py
1667 python2 mirna_expression.py
1668 python mirna_annotation.py
1669 ls
1670 cd mirdeep2/
1671 ls
1672 exit
1673 htseq-count
1674 sudo apt-get remove python-htseq
1675 fastq_quality_filter -h
1676 fastx_collapser -h
1677 novoindex
1678 novoalign
1679 randfold
1680 RNAfold -h
1681 htseq-count
1682 pip install HTSeq==0.6.1
1683 wget https://files.pythonhosted.org/packages/3c/6e/f8dc3500933e036993645c3f854c4351c9028b180c6dcececde944022992/HTSeq-0.6.1p1.tar.gz
1684 tar xvvzf HTSeq-0.6.1p1.tar.gz
1685 numpy
1686 novoindex
1687 novoalign
1688 cd mirPRo.1.1.4/
1689 ls
1690 cd ..
1691 cd novocraft/
1692 ls
1693 cd ..
1694 pip install numpy
1695 pip install --upgrade pip
1696 sudo pip install --upgrade pip
1697 pip install pysam
1698 pysam
1699 pySam
1700 conda config --add channels r
1701 conda config --add channels bioconda
1702 conda install pysam
1703 conda install numpy
1704 cd HTSeq-0.6.1p1/
1705 python setup.py build
1706 ls
1707 python2 setup.py build
1708 python setup.py install
1709 python2 setup.py install
1710 sudo python2 setup.py install
1711 cd ..
1712 htseq-count
1713 novoindex
1714 RNAfold -h
1715 htseq-count
1716 gcc -v
1717 g++ -v
1718 ls
1719 rm HTSeq-0.6.1p1.tar.gz
1720 cd mirPRo.1.1.4/
1721 pwd
1722 cd bin/
1723 pwd
1724 /home/siva/mirPRo.1.1.4/bin
1725 export PATH=$PATH:/home/siva/mirPRo.1.1.4/bin
1726 /home/siva/mirPRo.1.1.4/bin
1727 cd ..
1728 cd Documents/microRNA_data/
1729 ls
1730 bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1731 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1732 pip install pysam
1733 python3 -m venv env
1734 source ./env/bin/activate
1735 pip install pysam
1736 python3 -m venv env
1737 exit
1738 cd /home/siva/Documents/microRNA_data
1739 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1740 pip install numpy
1741 cd ..
1742 cd HTSeq-0.6.1p1/
1743 python setup.py build/
1744 python2 setup.py build/
1745 python2 setup.py build
1746 python2 setup.py install
1747 python setup.py build
1748 sudo python2 setup.py build
1749 sudo python2 setup.py install
1750 cd ..
1751 cd Documents/microRNA_data/
1752 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1753 samtools
1754 conda install -c bioconda htseq
1755 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1756 conda install samtools=1.9 -y
1757 samtools
1758 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1759 sudo apt-get remove python-htseq
1760 sudo apt autoremove python-htseq
1761 htseq-count
1762 sudo apt autoremove python-htseq
1763 htseq
1764 samtools
1765 sudo apt autoremove htseq
1766 sudo apt-get autoremove --purge python-htseq
1767 sudo apt-get autoremove python-htseq
1768 htseq-count
1769 htseq -h
1770 htseq-count -h
1771 htseq-count --version
1772 locate htseq-count
1773 conda remove htseq-count
1774 rm -rf ~/anaconda3
1775 locate htseq-count
1776 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1777 cd ..
1778 cd mirdeep2/
1779 perl install
1780 perl install.pl
1781 exit
1782 cd Documents/
1783 ls
1784 cd microRNA_data/
1785 ls
1786 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1787 randfold
1788 sudo apt-add-repository ppa:j-4/vienna-rna
1789 sudo apt-get install vienna-rna
1790 cd ..
1791 cd squid-1.9g/
1792 ./configure
1793 make
1794 make check
1795 make install
1796 sudo make
1797 sudo make install
1798 make
1799 cd ..
1800 ls
1801 tar xzvf randfold-2.0.tar.gz
1802 cd randfold-2.0/
1803 make
1804 apt-get install pkg_resources
1805 apt-get install python-setuptools
1806 sudo apt update && apt upgrade
1807 exit
1808 cp randfold /usr/local/bin
1809 exit
1810 cd ViennaRNA-2.4.16/
1811 ./configure
1812 make
1813 randfold
1814 locate htseq-count
1815 pip install pysam
1816 sudo apt-get install gcc
1817 sudo apt-get install make
1818 sudo apt-get update
1819 sudo pip install pysam
1820 cd ..
1821 cd Documents/microRNA_data/
1822 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1823 ls /usr/bin/python*
1824 sudo apt-get remove python3
1825 ls /usr/bin/python*
1826 apt --fix-broken install
1827 sudo apt --fix-broken install
1828 sudo apt autoremove python3
1829 ls /usr/bin/python*
1830 sudo apt install gnome
1831 ls /usr/bin/python*
1832 sudo apt autoremove python
1833 ls /usr/bin/python*
1834 sudo apt-get autoremove python
1835 python --version
1836 python -V
1837 sudo apt-get update
1838 cd /
1839 wget https://repo.anaconda.com/archive/Anaconda3-2020.11-Linux-ppc64le.sh
1840 sudo
1841 cat /etc/os-release
1842 sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6
1843 sha256sum /path/filename
1844 Get-FileHash filename -Algorithm SHA256
1845 ls
1846 cd home/
1847 ls
1848 cd siva/
1849 ls
1850 cd ..
1851 pwd
1852 cd siva/
1853 ls
1854 gzip PsFCIV_2.5.zip
1855 gunzip PsFCIV_2.5.zip.gz
1856 sha256sum PsFCIV_2.5.ps1
1857 ls
1858 bash Anaconda3-2020.11-Linux-ppc64le.sh
1859 ls
1860 bash Miniconda2-latest-Linux-x86_64.sh
1861 conda update conda
1862 conda init fish
1863 conda list
1864 pwd
1865 cd miniconda2/
1866 cd bin/
1867 pwd
1868 /home/siva/miniconda2/bin
1869 export PATH=/home/siva/miniconda2/bin
1870 export PATH=/home/siva/miniconda2/bin:$PATH
1871 conda
1872 conda list
1873 conda init fish
1874 conda update conda
1875 conda install pysam
1876 cd ..
1877 ls /usr/bin/python*
1878 pwd
1879 ls
1880 sudo apt-get update
1881 export PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
1882 ls
1883 sudo apt-get update
1884 ls /usr/bin/python*
1885 alias python='/usr/bin/python2.7
1886 . ~/.bashrc
1887 exot
1888 exit
1889 ls /usr/bin/python*
1890 python --versoin
1891 python --version
1892 update-alternatives --list python
1893 sudo apt-add-repository ppa:j-4/vienna-rna
1894 fastq_quality_filter -h
1895 fastx_collapser -h
1896 novoindex
1897 cd novocraft/
1898 ls
1899 pwd
1900 /home/siva/novocraft
1901 export PATH=$PATH:/home/siva/novocraft
1902 novoindex
1903 novoalign
1904 randfold
1905 locate randfold
1906 pwd
1907 cd ..
1908 RNAfold -h
1909 htseq-count
1910 pip install HTSeq==0.6.1p1
1911 sudo pip install HTSeq==0.6.1p1
1912 htseq-count
1913 sudo apt-get install pkg_resources
1914 pip install setuptools
1915 sudo apt-get install pkg_resources
1916 apt-get install python-setuptools
1917 sudo
1918 sudo -s
1919 sudo pip install HTSeq==0.6.1p1
1920 htseq-count
1921 RNAfold -h
1922 randfold
1923 cd randfold-2.0/
1924 make
1925 cd ..
1926 cd randfold_src/
1927 cd src/
1928 make
1929 randfold
1930 path
1931 touch PATH
1932 $PATH
1933 cp randfold /usr/local/bin
1934 sudo -s
1935 randfold
1936 ls
1937 rm randfold-2.0.tar.gz
1938 rm randfold-2.0
1939 rm -r randfold-2.0
1940 ls
1941 randfold
1942 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1943 pwd
1944 mv -r mirPro_results/ /home/siva/Documents/microRNA_data
1945 mv mirPro_results/ /home/siva/Documents/microRNA_data
1946 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> /mirPro_results/wt-Control-1.txt
1947 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> mirPro_results/wt-Control-1.txt
1948 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> ./mirPro_results/wt-Control-1.txt
1949 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> ./mirPro_results/wt_Control_1.txt
1950 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> mirpro_wt_Control_1.txt
1951 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> mirpro_wt_Control_2.txt
1952 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> mirpro_wt_Control_3.txt
1953 cd Documents/microRNA_data/
1954 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-2.fastq
1955 /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-2.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1956 sudo qpt-get update
1957 sudo nano /etc/NetworkManager/NetworkManager.conf
1958 sudo service network-manager restart
1959 sudo touch /etc/NetworkManager/conf.d/10-globally-managed-devices.conf
1960 sudo systemct1 restart NetworkManager
1961 sudo dhclient
1962 sudo apt-get update
1963 sudo apt-get upgrade
1964 sudo snap install notepad-plus-plus
1965 sudo apt-get upgrade
1966 sudo apt-get update
1967 nohup /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-2.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx
1968* nohup /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-Control-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-2.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k18-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/wt-ABA-1.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/abi1-ABA-3.fastq -i /home/siva/Documents/microRNA_data/TRIMMED/m3k17-ABA-2.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx >mirpro_scipt.txt 2>ran_scrip.txt
1969 history >hist.txt
1970 pwd
1971 cd Documents/Webinar/
1972 mv * /home/siva/Documents/
1973 cd ..
1974 rmdr Webinar/
1975 rm Webinar/
1976 rm -r Webinar/
1977 cd microRNA_data/
1978 ls
1979 scp -r fastX_toolkit_STATUS/ [email protected]:/microRNA_sequencing
1980 scp -r fastX_toolkit_STATUS/ [email protected]
1981 sftp -r fastX_toolkit_STATUS/ [email protected]
1982 ssh transfer
1983 sftp
1984 pwd
1985 ssh [email protected]
1986 ssh [email protected]
1987 sudo apt get-update && sudo apt-get upgrade
1988 sudo apt-get update && sudo apt-get upgrade
1989 ububtu --version
1990 ubuntu --version
1991 chdsk
1992 lsb_release -a
1993 uname -mrs
1994 sudo apt list --upgradable
1995 sudo apt upgrade
1996 exit
1997 cd Documents/microRNA_data/
1998 ls
1999 history 2>ran_script.txt
2000 history &> ran_script.txt