Comments (1)
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!
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Related Issues (20)
- What is the difference between "absolute peak summit" and "summit position" in narrowPeak format? HOT 1
- Feat: Enhanced clarification of the specific definition of BEDPE as used by MACS HOT 1
- Feat: Reduction of memory consumption HOT 3
- Q: HMMRATAC output and options for _summit.bed HOT 1
- Feat: Built-in scoring for HMMRATAC HOT 1
- Q: HMMRATAC producing too many peaks HOT 10
- Bug: undefined symbol: __pow_finite HOT 3
- Q: HMMRATAC reproducibility HOT 2
- Q: how to use MACS3 for ATAC seq with "himmratac" option? HOT 2
- Bug: Callvar throws an error when run on broadPeak file HOT 15
- Q: impact of sequencing throughput on peak calling HOT 4
- Setting cut-off when using logFE bigWig files from bdgcmp
- Q: How to use HMMRATAC to give us a narrow peak file and have signalValue, p and q-value ? HOT 1
- Bug: OverflowError when running hmmratac
- Number of de-duplicated reads indicated by filterdup log does not match number of lines in output BED file.
- Feat: Add --call-summits option in MACS3 bdgpeakcall?
- Q: using macs3 to detect peaks on long-read readings
- MACS3 callpeak does not create UCSC Browser ready peak files HOT 1
- Better cutoff levels control for bdgcallpeak cutoff-analysis HOT 1
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