PCR duplicates detected from different Genrich runs

[elenichri]

Hello! I am mapping my trimmed Fastq files to the human genome hg38 using bowtie2. Then I use Genrich to call peaks and mark the PCR duplicates. I then remove the duplicates from my .bam files using the pcrDup file generated by Genrich. I was wondering whether I get different pcrDup files for different Genrich parameters, not related to the duplicates...for example if I change the threshold of the q-value or the auc, do I end up with a different set of PCR duplicates?

Thank you in advance!

[jsh58]

Thanks for the question. Alignment parsing is entirely separate from peak-calling, so changing peak-calling parameters has no effect on the PCR duplicates identified by Genrich. See also the description of the -X option here.

[elenichri]

Thank you very much!