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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
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The production of *peaks_rmBlacklist.narrowPeak files #279

Open tan200000000 opened 3 months ago

tan200000000 commented 3 months ago

Hi, when I check the pepatac log, I find this command: bedtools intersect -a /data3/01.projects/GROUP01043/10.ATAC_seq_test/poj5/pepatac/mas1/peak_calling_mm10/mas1_peaks_normalized.narrowPeak -b /data3/01.projects/GROUP01043/10.ATAC_seq_test/poj5/pepatac/mas1/raw/mm10_blacklist.bed -v > /data3/01.projects/GROUP01043/10.ATAC_seq_test/poj5/pepatac/mas1/peak_calling_mm10/mas1_peaks_rmBlacklist.narrowPeak, but I find the size of the _peaks_rmBlacklist.narrowPeak file in my result is actully larger than the _peaks_normalized.narrowPeak file: image Then I rerun the command independently I found the size of rmBlacklist.narrowPeak file become smaller, and factually become the same as the *_peaks_normalized.narrowPeak file and they have the same md5. I dont know why this happened, thanks very much if anybody could answer me.

tan200000000 commented 3 months ago

this picture is from a parllel project becuse I change some files of the origin project