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6.2 years ago
dcheng1
•
0
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!
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