Open MinaMyr opened 2 months ago
Hello and thanks for making this resource. I am commenting here to track this since I'm having the same issue: no narrowPeak output from the hmmratac using mapped .bam files with the following code:
macs3 hmmratac \ -i D*rep1_paired.sorted.bam \ *rep2_paired.sorted.bam \ --outdir directory \ -n output_name \ -u 20 \ -l 10 \ -c 2
I previously ran the with the --cutoff-analysis-only
flag prior to entering the -u -l -c params. I'm using version 3.0.1 in a conda environment with a SGE scheduler. There are no errors in the output. Here are the last lines of the run output:
INFO @ 14 Jun 2024 17:06:54: [7795 MB] # Write the output... INFO @ 14 Jun 2024 17:09:30: [7795 MB] # Write accessible regions in a gappedPeak file: *accessible_regions.gappedPeak
Use case Hello I want to do peak calling on my ATAC seq data, and for that I use, callpeak and hmmratac.
Describe the problem My problem here is with hmmratac;
I use this command
macs3 hmmratac -f BAM -i RES/atac/try_1/04-NobiasedRegions/ATAC20_D0_rep1_hg38_sort_dedup_biasedRegions.bam -u 15 -l 5 -c 100 -n RES/atac/try_1/06-PeakCalling/hmmratac_narrow/ATAC20_D0_rep1
I read in the doc that we should have a narrow peak file format but I have an *_accessible_regions.gappedPeak format which is not what I want. For the rest of my analysis I need a narrow peak format.Describe the solution you tried So I tried to create my narrow peak file from the gappedPeak, by hand, but the trouble I am now having is that for the signal value, p-value and q-value are equals to 0 (I think like this comment said it is intentional https://github.com/macs3-project/MACS/issues/592#issuecomment-1981383873 ). Here is what my file look like;
I don't really know what to do now, since signal Value p-value and q-value are important for the rest of my analysis. Thank you in advance !