Question: Compare bedgraphs of two treatments after MACS2 callpeak.. do I need SPMR?
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gravatar for Stefan.Kurtenbach
2.5 years ago by
Stefan.Kurtenbach0 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 • 1.1k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Stefan.Kurtenbach0
0
gravatar for Stefan.Kurtenbach
2.5 years ago by
Stefan.Kurtenbach0 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 COMMENTlink written 2.5 years ago by Stefan.Kurtenbach0
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