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filter_alignqc_res.R
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source('scDataAnalysis_Utilities.R')
`%notin%` = Negate(`%in%`)
score.thr = 2
## for AF9 (MLLT3) ####
for(sampleName in c('1154', 'PAZGKI', 'PAZBGV')){
dd = fread(paste0('AlignQC/Chimera_Output/', sampleName, '_chimera.bed.gz'),
skip = 1)
names(dd)[c(1:4, 10)] = c('chr', 'start', 'end', 'readname', 'score')
dd[, 'len' := end-start]
if(sampleName != 'MLLr1154') dd[, 'chr' := paste0('chr', chr)]
dd1 = dd[chr == 'chr11' & score >= score.thr]
dd1 = dd1[(start >= 118481810 & start < 118481830) | (end >= 118481810 & end < 118481830)]
dd2 = dd[ chr == 'chr9' & start >= 20341669 & end <= 20622499 & score >= score.thr]
sele.reads = intersect(dd1$readname, dd2$readname)
dd.sele = dd[readname %in% sele.reads]
message(paste0(sampleName, ': detected ', length(sele.reads), ' fusion reads!'))
outFile = paste0('MetaData/scRNA/LongRead/', sampleName, '_alignqc_filtered_fusion.txt')
write.table(dd.sele, file = outFile,
row.names = F, quote = F, sep = '\t')
}
## for AF4 ####
for(sampleName in c('PAYWKL', 'PAYYNY', 'PAYSBA', 'PAYKGI', 'PAYZWN ')){
chimera.file = paste0('AlignQC/Chimera_Output/', sampleName, '_chimera.bed.gz')
if(!file.exists(chimera.file)) next
dd = fread(chimera.file, skip = 1)
names(dd)[c(1:4, 10)] = c('chr', 'start', 'end', 'readname', 'score')
dd[, 'len' := end-start]
dd[, 'chr' := paste0('chr', chr)]
score.thr = 2
dd1 = dd[chr == 'chr11' & score >= score.thr]
dd1 = dd1[(start >= 118481810 & start < 118481830) | (end >= 118481810 & end < 118481830)]
dd2 = dd[ chr == 'chr4' & start >= 87006988 & end <= 87141038 & score >= score.thr]
sele.reads = intersect(dd1$readname, dd2$readname)
dd.sele = dd[readname %in% sele.reads]
message(paste0(sampleName, ': detected ', length(sele.reads), ' fusion reads!'))
outFile = paste0('MetaData/scRNA/LongRead/', sampleName, '_alignqc_filtered_fusion.txt')
write.table(dd.sele, file = outFile,
row.names = F, quote = F, sep = '\t')
}
## for ENL ####
for(sampleName in c('PAYYBG', 'PAZBSZ', 'PAZFPH', 'PAYWJZ', 'PAYUZJ')){
chimera.file = paste0('AlignQC/Chimera_Output/', sampleName, '_chimera.bed.gz')
if(!file.exists(chimera.file)) next
dd = fread(chimera.file, skip = 1)
names(dd)[c(1:4, 10)] = c('chr', 'start', 'end', 'readname', 'score')
dd[, 'len' := end-start]
if(sampleName %notin% c('PAYUZJ')) dd[, 'chr' := paste0('chr', chr)]
dd1 = dd[chr == 'chr11' & score >= score.thr]
dd1 = dd1[(start >= 118481810 & start < 118481830) | (end >= 118481810 & end < 118481830)]
dd2 = dd[ chr == 'chr19' & start >= 6210381 & end <= 6279975 & score >= score.thr]
sele.reads = intersect(dd1$readname, dd2$readname)
dd.sele = dd[readname %in% sele.reads]
message(paste0(sampleName, ': detected ', length(sele.reads), ' fusion reads!'))
outFile = paste0('MetaData/scRNA/LongRead/', sampleName, '_alignqc_filtered_fusion.txt')
write.table(dd.sele, file = outFile,
row.names = F, quote = F, sep = '\t')
}
## for AF10 ####
for(sampleName in c( 'PAZBLA', 'PAYUZM')){
chimera.file = paste0('AlignQC/Chimera_Output/', sampleName, '_chimera.bed.gz')
if(!file.exists(chimera.file)) next
dd = fread(chimera.file, skip = 1)
names(dd)[c(1:4, 10)] = c('chr', 'start', 'end', 'readname', 'score')
dd[, 'len' := end-start]
dd1 = dd[chr == 'chr11' & score >= score.thr]
dd1 = dd1[(start >= 118481810 & start < 118481830) | (end >= 118481810 & end < 118481830)]
dd2 = dd[ chr == 'chr10' & start >= 21534232 & end <= 21743630 & score >= score.thr]
sele.reads = intersect(dd1$readname, dd2$readname)
dd.sele = dd[readname %in% sele.reads]
message(paste0(sampleName, ': detected ', length(sele.reads), ' fusion reads!'))
outFile = paste0('MetaData/scRNA/LongRead/', sampleName, '_alignqc_filtered_fusion.txt')
write.table(dd.sele, file = outFile,
row.names = F, quote = F, sep = '\t')
}
## for EPS15 ####
for(sampleName in c( 'PAYLNH', 'PAYZLC')){
chimera.file = paste0('AlignQC/Chimera_Output/', sampleName, '_chimera.bed.gz')
if(!file.exists(chimera.file)) next
dd = fread(chimera.file, skip = 1)
names(dd)[c(1:4, 10)] = c('chr', 'start', 'end', 'readname', 'score')
dd[, 'len' := end-start]
if(sampleName != 'PAYLNH') dd[, 'chr' := paste0('chr', chr)]
dd1 = dd[chr == 'chr11' & score >= score.thr]
dd1 = dd1[(start >= 118481810 & start < 118481830) | (end >= 118481810 & end < 118481830)]
dd2 = dd[ chr == 'chr1' & start >= 51354263 & end <= 51519266 & score >= score.thr]
sele.reads = intersect(dd1$readname, dd2$readname)
dd.sele = dd[readname %in% sele.reads]
message(paste0(sampleName, ': detected ', length(sele.reads), ' fusion reads!'))
outFile = paste0('MetaData/scRNA/LongRead/', sampleName, '_alignqc_filtered_fusion.txt')
write.table(dd.sele, file = outFile,
row.names = F, quote = F, sep = '\t')
}
## for PSMF1 ####
for(sampleName in c( 'PAYZVY')){
chimera.file = paste0('AlignQC/Chimera_Output/', sampleName, '_chimera.bed.gz')
if(!file.exists(chimera.file)) next
dd = fread(chimera.file, skip = 1)
names(dd)[c(1:4, 10)] = c('chr', 'start', 'end', 'readname', 'score')
dd[, 'len' := end-start]
dd[, 'chr' := paste0('chr', chr)]
dd1 = dd[chr == 'chr11' & score >= score.thr]
dd1 = dd1[(start >= 118481810 & start < 118481830) | (end >= 118481810 & end < 118481830)]
dd2 = dd[ chr == 'chr20' & start >= 1113263 & end <= 1167782 & score >= score.thr]
sele.reads = intersect(dd1$readname, dd2$readname)
dd.sele = dd[readname %in% sele.reads]
message(paste0(sampleName, ': detected ', length(sele.reads), ' fusion reads!'))
outFile = paste0('MetaData/scRNA/LongRead/', sampleName, '_alignqc_filtered_fusion.txt')
write.table(dd.sele, file = outFile,
row.names = F, quote = F, sep = '\t')
}
## fusion for HD ####
for(sampleName in c( 'HD2111_CD34', 'HD2689_Live')){
chimera.file = paste0('AlignQC/Chimera_Output/', sampleName, '_chimera.bed.gz')
if(!file.exists(chimera.file)) next
dd = fread(chimera.file, skip = 1)
names(dd)[c(1:4, 10)] = c('chr', 'start', 'end', 'readname', 'score')
dd[, 'len' := end-start]
dd1 = dd[chr == 'chr11' & score >= score.thr]
dd1 = dd1[(start >= 118481810 & start < 118481830) | (end >= 118481810 & end < 118481830)]
dd2 = dd[ chr != 'chr11' & score >= score.thr]
sele.reads = intersect(dd1$readname, dd2$readname)
dd.sele = dd[readname %in% sele.reads]
message(paste0(sampleName, ': detected ', length(sele.reads), ' fusion reads!'))
outFile = paste0('MetaData/scRNA/LongRead/', sampleName, '_alignqc_filtered_fusion.txt')
write.table(dd.sele, file = outFile,
row.names = F, quote = F, sep = '\t')
}
## for WT ####
sampleNames = c("PAYWJZ", "PAZGKI", "PAYUZM", "1154",
"PAYKGI", "PAZBSZ", "PAYWKL", "PAYSBA",
"PAZBLA", "PAYZLC", "PAYLNH", "PAYUZJ",
"PAYYBG", "PAZFPH", "PAYYNY", "PAZBGV",
"PAYZVY", "PAYZWN ", "HD2111_CD34", 'HD2689_Live')
for(sampleName in sampleNames){
long.read.file = paste0('AlignQC/Chimera_Output/', sampleName, '_best.sorted.bed.gz')
chimera.file = paste0('AlignQC/Chimera_Output/', sampleName, '_chimera.bed.gz')
if(!file.exists(long.read.file)) next
dd.trans = fread(chimera.file, skip = 1, select = c(1:4, 10))
names(dd.trans) = c('chr', 'start', 'end', 'readname', 'score')
dd = fread(long.read.file, skip = 1, select = c(1:4, 10))
names(dd) = c('chr', 'start', 'end', 'readname', 'score')
dd[, 'len' := end-start]
dd.trans[, 'len' :=end-start]
if(sampleName %notin% c('1154', 'PAZBLA', 'PAYLNH', 'HD2111_CD34',
'HD2689_Live', 'PAYUZJ', 'PAYUZM')) {
dd[, chr := paste0('chr', chr)]
dd.trans[, chr := paste0('chr', chr)]
}
dd0 = dd[chr == 'chr11']
dd0 = dd0[(start >= 118481713 & start <= 118482093) | (end >= 118481713 & end <= 118482093)]
dd0.trans = dd.trans[chr == 'chr11']
dd0.trans = dd0.trans[(start >= 118481713 & start <= 118482093) | (end >= 118481713 & end <= 118482093)]
dd.pcr = rbind(dd0, dd0.trans[dd0.trans$readname %notin% dd0$readname, ])
outFile0 = paste0('MetaData/scRNA/LongRead/', sampleName, '_alignqc_reads2PCR.txt')
write.table(dd.pcr, file = outFile0,
row.names = F, quote = F, sep = '\t')
dd1 = dd[chr == 'chr11' & score >= score.thr]
dd1 = dd1[(start >= 118490129 & start < 118523917) | (end >= 118490129 & end < 118523917)]
dd2 = dd[chr != 'chr11' & score >= score.thr]
dd1 = dd1[readname %notin% dd2$readname]
message(paste0(sampleName, ': detected ', nrow(dd1), ' wt reads!'))
outFile = paste0('MetaData/scRNA/LongRead/', sampleName, '_alignqc_filtered_wt.txt')
write.table(dd1, file = outFile,
row.names = F, quote = F, sep = '\t')
}