Question: Narrow & Broad peaks from 'macs2 bdgdiff'
gravatar for anu014
5 months ago by
anu014140 wrote:

Hello Biostars,

Can anyone tell me how to give narrow & broad peak parameters in 'macs2 bdgdiff' program, as we can mention in macs2 callpeak with '--call-summits' for narrow & '--broad' for broad peaks.?

Thanks in advance. :)

ADD COMMENTlink modified 5 months ago by jared.andrews07660 • written 5 months ago by anu014140
gravatar for jared.andrews07
5 months ago by
Washington University in St. Louis
jared.andrews07660 wrote:

There are no parameters like that for bdgdiff, which just looks at the raw bedgraph pileups to determine differentially bound regions. Personally, I've found it doesn't do all that great a job of it either.

If you want to see which peaks called have significantly different signal between two files, I'd recommend MAnorm which will take two peak files and two reads files, derive a consensus peak set, and tell you which of the peaks are significantly different between the two samples. Using this method, you could feed in the summits or broad peaks as your peak files.

ADD COMMENTlink written 5 months ago by jared.andrews07660

Yes, MAnorm sounds better. The MAnorm's manual says that it gives M & A values too. Can I say A is somewhat equivalent to fold change in macs2?

ADD REPLYlink written 5 months ago by anu014140

The M value is more akin to fold change, though it's a better idea to consider it as a measure of the magnitude of the change between the two samples. Significance is great, but a significant yet small change between the two samples may be biologically irrelevant - using the magnitude of the difference helps eliminate false positives seen using the p-value alone. You can use the p-value output and the M value (positive for peaks enriched in sample 1, negative for peaks enriched in sample 2) to define your different lists of differentially bound peaks.

ADD REPLYlink written 5 months ago by jared.andrews07660
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