Entering edit mode
6 months ago
Marcos
•
0
Hello,
I am trying to run macs2 peak calling on a bed file, but whenever I specify the genome size (-gsize or -g) as mm or 1.87e9, I get empty bed, excel, and narrowpeak files. However, when I don't include -gsize or default to hs, files are produced that aren't empty. I was wondering if anyone had any suggestions on solutions? Is this something about the bed file or the code I am using?
Input for empty file output with -gsize mm:
$ macs2 callpeak -t 3tongueWT3_H3K4me3.bed -f BED --gsize mm -n 3tongueWT3_H3K4me3 --outdir ~ --nomodel --extsize 200
Input for non-empty file output with -gsize hs:
$ macs2 callpeak -t 3tongueWT3_H3K4me3.bed -f BED --gsize hs -n 3tongueWT3_H3K4me3_hs --outdir ~ --nomodel --extsize 200
Additional info: Code finishes to completion without any crashes when producing the empty files. Bed files are based on mouse models.
