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jsh58 / Genrich

Detecting sites of genomic enrichment
MIT License
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Input control DNA #32

Closed keenhl closed 4 years ago

keenhl commented 4 years ago

According the documentation, input control samples are not required to run Genrich. My question is two fold: how does the Genrich algorithm deal with not having a reference control and, importantly, does having a control sample significantly improve the performance of Genrich. Thank you for your help.

Optional files

-c Input SAM/BAM file(s) for control sample(s)

jsh58 commented 4 years ago

Thanks for the questions. The method for calculating the control pileup value, with or without a control sample, is explained here. Having a control sample helps to limit false positive peaks, such as high mappability regions that show enrichment under any condition.