search

jsh58 / Genrich

Detecting sites of genomic enrichment
MIT License
182 stars 27 forks source link

Number of peaks fall after including input DNA control #94

Closed keenhl closed 1 year ago

keenhl commented 2 years ago

When I include the input DNA control (-c option), I only get a few hundred called peaks. However, leaving all the other parameters the same, if I do not include the input DNA, the number of peaks goes up about 10 fold. Is this expected, that the number of peaks would fall so much after including the input DNA control?

Thanks for your help.

jsh58 commented 1 year ago

It is expected that specifying a control sample will increase the control pileup value at some genomic positions, and thus result in fewer peaks. Beyond that, I cannot comment on the particulars of your experiment.