procReadsJ.pl -- Processing a duplicate-removed JSAM file (rmDup) of a chromosome (Dr. JH Lee's format) to generate the chromosome specific SNV list and the bedgraph file. The output files are used as input files for the ASARP pipeline. See procReads for the version on standard SAM files.
This is part of the full pre-processing:
1. rmDup (removing PCR duplicates for SAM files (including Dr. JH Lee's SAM format))
2. mergeSam (merging SAM files if there are independent duplicates)
3. procReads (processing SAM files to get SNV read counts and generate bedgraph files)
USAGE:
perl procReadsJ.pl chr input_sam_file input_snvs output_snvs output_bedgraph is_paired_end [discarded_read_pos]
NOTE:
the read processing script is for Dr. Jae-Hyung Lee's 20-attribute SAM file output format, used in RNA-editing or allele specific expression (ASE) studies. If you use standard 10-attribute SAM files, you can use procReads.pl provided in this pipeline, samtools or bedtools
The complete documentation with the same arguments and usage can be found in procReads The only difference between procReadsJ.pl and procReads.pl is that they work on jsam and standard sam (jsam also treated as standard sam) files respectively.
This pipeline is free software; you can redistribute it and/or modify it given that the related works and authors are cited and acknowledged.
This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.
Cyrus Tak-Ming CHAN
Xiao Lab, Department of Integrative Biology & Physiology, UCLA