Q: conversion of output files to UCSC track hub format?

[maximilianh]

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]

Hi @maximilianh,
Please take a look at the test/standard_results_ 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!