Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Compare bedgraphs of two treatments after MACS2 callpeak.. do I need SPMR?
0
gravatar for Stefan.Kurtenbach
2.6 years ago by
Stefan.Kurtenbach • 0
Stefan.Kurtenbach • 0 wrote:

Hey y'all, I'd appreciate your help here!

Do I really need to use the SPMR option in MACS2 to compare the bedgraph outputs to each other? Say same cell line, two conditiones, I run MACS2 for each, using the input as a control. Then i display the bedgraph files in UCSC. Can I compare those like this visually, or is that really only true if the SPMR option is set?

Is there no SPMR option for MACS2 on galaxy?
galaxy spmr macs2 chip-seq • 1.2k views
ADD COMMENT • link •
modified 2.6 years ago • written 2.6 years ago by Stefan.Kurtenbach • 0
0
gravatar for Stefan.Kurtenbach
2.6 years ago by
Stefan.Kurtenbach • 0
Stefan.Kurtenbach • 0 wrote:

Answering my own question in case someone stumbles upon the same problem...

I think you can't compare them. To do so, you'll need to run MACS2 with the -B -SPMR commands, which will normalize the files to million reads.
ADD COMMENT • link written 2.6 years ago by Stefan.Kurtenbach • 0
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour