MACS2 gives negative estimated fragment length
Hi, I have two ChIP-seq replicates and their peak profile looks very similar in genome browser.
When I use macs2 to call peaks, rep2 has a 345 bp of estimated fragment length, but the est. fragment len. of rep1 is -5. I wonder how this happened since these two replicates seems to correlates with each other well. Any opinions are greatly appreciated!
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Please provide the full command and what protein target you ChIPed.
I target histone modification H3K4me3.
I used AQUAS chipseq pipeline, so I didn't type in any macs2 command, but I think the command is:
callpeak -t -c -f BED -n -g hs -p 0.01 --nomodel --shift 0 --extsize 345 --keep-dup all -B --SPMR