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

[bentyeh]

The "Advanced Step-by-step peak calling using MACS3 commands" tutorial [webpage, source] has 2 issues:

1. The tutorial claims that the 2 test files, CTCF_ChIP_200K.bed.gz and CTCF_Control_200K.bed.gz, can be found "in the MACS3 GitHub repository in the test directory." However, there are no such files currently in the master branch of the MACS GitHub repository.

   • Instead was able to find them online elsewhere, such as at https://github.com/taoliu/MACS/raw/c854599457a14a6da97ec45f478939af1397ec5c/test/CTCF_ChIP_200K.bed.gz and https://github.com/taoliu/MACS/raw/c854599457a14a6da97ec45f478939af1397ec5c/test/CTCF_Control_200K.bed.gz.

2. The macs3 pileup -i <*.bed> ... commands currently (using macs3 3.0.3) raise an error

   ERROR @ 26 Feb 2025 21:53:52: [34 MB] Format "AUTO" cannot be recognized!
   

   and seem to fail to automatically detect the BED input format. Adding the option -f BED resolves the issue.

   As I'm new to MACS, I'm not sure if this is simply a documentation issue (i.e., the commands in the tutorial should be updated to include the -f BED option) or if this reflects a bug in the macs3 pileup program.

[taoliu]

@bentyeh Thanks for the feedback! I need to revise that document. Stay tuned.