Hi everyone, I had a question regarding the filtering steps where the aligned reads are filtered. Is there anywhere that I can find the reasons for selecting the following filtering criteria in the chipseq pipeline? I am curious to know the reasoning behind it.

Filtering to remove:
reads mapping to blacklisted regions (SAMtools, BEDTools)
reads that are marked as duplicates (SAMtools)
reads that are not marked as primary alignments (SAMtools)
reads that are unmapped (SAMtools)
reads that map to multiple locations (SAMtools)
reads containing > 4 mismatches (BAMTools)
reads that have an insert size > 2kb (BAMTools; paired-end only)
reads that map to different chromosomes (Pysam; paired-end only)
reads that arent in FR orientation (Pysam; paired-end only)
reads where only one read of the pair fails the above criteria (Pysam; paired-end only)

Additionally is there a flag that I can use when running the pipeline, to turn off these filtering steps, to see if the results change?