Question: MACS2 gives negative estimated fragment length
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gravatar for dcheng1
2.2 years ago by
dcheng10
dcheng10 wrote:

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!

chip-seq • 774 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by dcheng10

Please provide the full command and what protein target you ChIPed.

ADD REPLYlink written 2.2 years ago by ATpoint34k

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

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by dcheng10
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