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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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Same number of Raw Peaks and Naive Overlap Peaks #68

Closed ajlawler closed 6 years ago

ajlawler commented 7 years ago

Hi all,

Thanks for putting this together. When I run my PE replicate samples, I am getting the same (exact) number for Raw Peaks and Naive Overlap Peaks in the ATAqc html report, and 0 IDR peaks. In fact, the entire Peak Statistics section is identical between the Rep 1 and Rep 2 html reports. The other sections of the reports are specific to each sample. I have verified that I called the correct read 1 and read 2 files. I ran a different set of replicates through the pipeline and had the same problem. Is there something I might be doing wrong?

leepc12 commented 7 years ago

Can you email those HTML reports to me (leepc12 at gmail dot com)?

leepc12 commented 7 years ago

Yes, "Raw peaks" is identical to "Naive overlap peaks" in the ATAQC report. They are actually naive overlap peaks (not raw peaks directly called from MACS2). This naming can be a bit confusing. We will change it in the next version of the pipeline.