Issues

• Bugs found by running ~27,000 macs3 commands on main (6dbd9a2): 2 regressions from #737, a total miscount, and 15 older crashes

  macs3-project/MACS#757 · Filter by author jmschrei opened on Oct 4, 2026
  1

  

• Bug: narrowPeak File fails to be saved

  Bug Report
  macs3-project/MACS#730 · Filter by author SportyScientist opened on Jun 1, 2026
  1

• Bug: thick background Poisson p-value at peak-desert region from ATAC-seq.

  Bug Report
  macs3-project/MACS#729 · Filter by author yang-kaist opened on May 7, 2026

• Q: BdgPeakcall output format

  General Question
  macs3-project/MACS#725 · Filter by author marinafloresp opened on Mar 19, 2026

• Q. How is fragment length 'd' calculated with --nomodel?

  macs3-project/MACS#722 · Filter by author swati375 opened on Feb 12, 2026
  3

• Q: Callpeak and bdgcmp q value computation

  General Question
  macs3-project/MACS#721 · Filter by author LinearParadox opened on Feb 4, 2026
  1

• Bug: HMMRATAC mode won't take -f FRAG input format

  Bug Report
  macs3-project/MACS#719 · Filter by author chrysania opened on Jan 26, 2026
  1

• Bug: macs3 hmmratac crashes with --save-likelihoods option

  Bug Report
  macs3-project/MACS#713 · Filter by author mosheolshansky-dot opened on Nov 6, 2025
  3

• Q/Feat: Additional clarity/control of HMMRATAC accessible region calling

  Feature Request
  macs3-project/MACS#711 · Filter by author mrendleman opened on Sep 11, 2025

• How does --scale-to {large,small} work

  macs3-project/MACS#710 · Filter by author leon945945 opened on Aug 15, 2025

• Q: MACS3 Broad Peak Cutoff Analysis

  General Question
  macs3-project/MACS#707 · Filter by author infurnoheat opened on Jul 18, 2025
  1

• Q: Guidance on enhancing MACS3 parameters.

  General Question
  macs3-project/MACS#706 · Filter by author fm504 opened on Jul 4, 2025

• Bug: Value too large to convert to unsigned char

  Bug Report
  macs3-project/MACS#705 · Filter by author ashwathkumar opened on Jun 26, 2025
  3

• Bug: macs3 hmmratac --cutoff-analysis-only always exits with exitcode 1

  Bug Report
  macs3-project/MACS#704 · Filter by author tellyalogicalguy opened on Jun 24, 2025

• Q: ImportError when use macs2

  General Question
  macs3-project/MACS#703 · Filter by author Tsssssssssssssssssssssssss opened on May 15, 2025
  2

• Q: HMMRATAC cutoff analysis need help with choosing cutoffs

  General Question
  macs3-project/MACS#701 · Filter by author budeer opened on May 8, 2025
  1

• Q: There is a problem when I use macs3 bdgpeakcall

  General Question
  macs3-project/MACS#700 · Filter by author GivingupCoke opened on Apr 28, 2025

• Bug: cannot install MACS3 by conda

  Bug Report
  macs3-project/MACS#699 · Filter by author Bencshan opened on Apr 12, 2025
  4

• Bug:

  Bug Report
  macs3-project/MACS#698 · Filter by author bbimber opened on Apr 7, 2025

• hmmratac: ValueError: Adjust --means and --stddev options and re-run command

  Bug Report
  macs3-project/MACS#697 · Filter by author bbimber opened on Apr 7, 2025
  3

• Q: split chromosomes

  General Question
  macs3-project/MACS#696 · Filter by author zhengluo-zz opened on Apr 4, 2025
  1

• Bug: pileup with -f FRAG yields OverflowError

  Bug Report
  macs3-project/MACS#695 · Filter by author jacob-greene opened on Mar 25, 2025
  2

  

• Documentation: Missing test files and errors when running commands from tutorial

  General Question
  macs3-project/MACS#693 · Filter by author bentyeh opened on Feb 27, 2025
  1

• Q: How many fragments are generally sufficient for hmmratac function?

  General Question
  macs3-project/MACS#687 · Filter by author leqi0001 opened on Feb 12, 2025
  3

• Q: ERROR: Could not build wheels for cykhash, which is required to install pyproject.toml-based projects

  General Question
  macs3-project/MACS#684 · Filter by author Eunbi9561 opened on Feb 3, 2025
  3