Q: How to use HMMRATAC to give us a narrow peak file and have signalValue, p and q-value ?

[MinaMyr]

Q: How to use HMMRATAC to give us a narrow peak file and have signalValue, p and q-value ?

[nickgladman]

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