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

[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!