Read_extractor it's a simple Linux script that uses Samtools to obtain reads from several genomic loci in a sorted and indexed BAM file, using a list of loci from a .csv file.
This script gets every read from the specified genomic location (formatted according to the reference genome used), and counts how many times it's repeated, to finally add that number in a new column.
-i: Path to input file. Must be a sorted and indexed BAM file.
-f: Path to csv file containing the list of loci to extract. You can easily format your loci to csv using Sed, e.g: if you have your loci in a calc or excel sheet, you can change the new line (\n) to comma (,) with sed ':a;N;$!ba;s/\n/,/g' inputfile > output.csv .
-s: Select sense or antisense strand. Works with SAM flags, select 0 for sense or 16 for antisense.
-r: Minimun number of reads to keep.
./Read_extractor.sh -i input_sorted.bam -f Loci.csv -s 0 > ./output/sense.tab
- Using
Read_extractor_individual.shwill generate one file for each locus in the loci file, it will put the output files in the working directory, don't add ">".
Your output should look like this one:
