repeSeq_scripts

repeseq_scripts is a collection of scripts used for the

1. Artificial generation of sequencing reads replicating a capture experiment of a 4 repeat “GGCCCC” probe within the human genome.
2. Alignment and repeat expansion quantification from repeSeq capture

Instructions

code_location=/Users/zacc/USyd/UMI_repeatexpansions/manuscript_scripts

1) Articifical read generation and alignment

${code_location}/launch_read_generator_align.pbs
# NOTE - artificial reads can be generated independently by ${code_location}/bash/read_generator_1.2.sh

2a) Collapse and trimming of sWGS & repeSeq

${code_location}/collapse_trim.sh

2b) Alignment and repeat expansion quantification of repeSeq using STRetch

${code_location}/repeSeq_STRetch.sh

2c) Intersections (overlap) between repeSeq and sWGS

${code_location}/bed_interesect_analysis.sh

2d) script for counting STR within reads

for i in *collapsed_trimmed_R1.fastq.gz;do
echo $i
zcat $i | awk 'NR%4==2' | grep "CCGGGG" | wc -l
zcat $i | awk 'NR%4==2' | grep "CCGGGGCCGGGG" | wc -l
done

2e) script for plotting sequencing metrics

${code_location}/general_plotting.R

2f) script for analysing enrichment of genomic features using LOLA

${code_location}/lola_analysis_repeseq.R