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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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Q: conversion of output files to UCSC track hub format? #621

Open maximilianh opened 4 months ago

maximilianh commented 4 months ago

Use case I work for UCSC and we sometimes get reports that MACS2 or MACS3 files are not valid to loading into our browser. I'd like to help write a converter from all the MACS2/3 output files to a UCSC track hub.

Describe the problem I am looking for a directory with all the different output formats of an example run.

Describe the solution you tried We have various command line programs and a conversion script that could be used here.

Additional context The resulting track hub could also be loaded into IGV, NCBI and Ensembl.

philippadoherty commented 4 months ago

Hi @maximilianh, Please take a look at the test/standardresults folders, the commands for these outputs are in test/cmdlinetest.

For example, the first test in cmdlinetest (below) will be associated with the **test/standard_results_callpeak_narrow/run_callpeak_narrow0*** files.

# callpeak
echo "1. callpeak"
echo "1.1 callpeak narrow"

mkdir ${OUTPUTDIR_PREFIX}_run_callpeak_narrow

macs3 callpeak -g 52000000 -t $CHIP -c $CTRL -n run_callpeak_narrow0 -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_narrow --cutoff-analysis &> ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0.log

Please let us know if you have additional questions along the way. Thanks!