angelosarmen

Q: Why is the default value of max-gap the detected read length?

1

Hi, I would like to use MACS2 for ATAC-seq. Could you please explain the reasoning behind the default value for max-gap being the detected read length (= tag size). Since...

BR: --modelonly true is ignored

2

**Describe the bug** Setting `--modelonly true` is ignored. **To Reproduce** `java -jar HMMRATAC_V1.2.10_exe.jar -b 65283_treat_rep1.chr22.20to30MB.bam -i 65283_treat_rep1.chr22.20to30MB.bam.bai -g hg19.chr22.genome --modelonly true` **Expected behavior** I would expect HMMRATAC to quit after...

BR: Overlapping peaks in the output

1

**Describe the bug** Some peaks in *.gappedPeak overlap. **To Reproduce** The following two peaks overlap in example output `65283_chr22_peaks.gappedPeak`: ``` chr22 37484220 37485340 chr22 37485300 37487330 ``` **Expected behavior** I...