MACS3 callpeak does not create UCSC Browser ready peak files

[callum-b]

The MACS3 docs state that callpeaks create Peak files that are compatible with the UCSC browser, but when I try to upload mine, the 7th-10th values raise errors. From the docs it looks like callpeaks is supposed ot create a track header in the file, but this is not the case.

Was this fixed in a later version? Did I miss an option for MACS3.0.0

command used: macs3 callpeak -f BED -t DATA/BED/CTCF_H3K9ac/H3K9ac_T7_neg_3_filterdup_filterchr.bed -c DATA/BED/CTCF_H3K9ac/Input_T7_neg_filterdup_filterchr.bed -n H3K9ac_T7_neg_3 --outdir DATA/PEAKS/CTCF_H3K9ac/ --nomodel --extsize 121 -g hs -q 0.01 2>snakemake_logs/macs3_callpeak/CTCF_H3K9ac_H3K9ac_T7_neg_3.log

• MACS Version 3.0.0

[taoliu]

Hi @callum-b You will have the UCSC required trackline annotation in the header of output files with '--trackline' option on.

For example: macs3 callpeak -f BED -t DATA/BED/CTCF_H3K9ac/H3K9ac_T7_neg_3_filterdup_filterchr.bed -c DATA/BED/CTCF_H3K9ac/Input_T7_neg_filterdup_filterchr.bed -n H3K9ac_T7_neg_3 --outdir DATA/PEAKS/CTCF_H3K9ac/ --nomodel --extsize 121 -g hs -q 0.01 --trackline 2>snakemake_logs/macs3_callpeak/CTCF_H3K9ac_H3K9ac_T7_neg_3.log

We will modify the document to correctly state this feature. Thank you!