Question: MACS2 gives negative estimated fragment length
0
gravatar for dcheng1
3 months 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 • 174 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by dcheng10

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

ADD REPLYlink written 3 months ago by ATpoint4.4k

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 3 months ago • written 3 months ago by dcheng10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1354 users visited in the last hour