Question: Convert DiffBind output to standard BED or NarrowPeak format
0
gravatar for rbronste
23 months ago by
rbronste260
rbronste260 wrote:

Trying to figure out how to convert a differentially called list from DiffBind into one of these standard formats?

narrowpeak chip-seq diffbind bed • 1.0k views
ADD COMMENTlink modified 4 months ago by corinne_hutfilz0 • written 23 months ago by rbronste260
2
gravatar for Rory Stark
23 months ago by
Rory Stark510
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark510 wrote:

You can generate bed files from a GRanges object (as returned by dba.report) using export.bed() from the rtracklayer package.

> library(rtracklayer)
> dbsites <- dba.report(myDBA, contrast=1, th=0.05)
> export.bed(dbsites,"dbsites.bed")
ADD COMMENTlink modified 23 months ago • written 23 months ago by Rory Stark510
0
gravatar for corinne_hutfilz
4 months ago by
corinne_hutfilz0 wrote:

I've a slightly more complicated version of this issue. I want to export a list of peaks that do not overlap within 4 groups (e.g. myDBA$onlyA or myDBA$AandC).

From dba.analyze I have 6 contrasts. Which options do I use for dba.report to generate a contrast resembling:

myDBA.OL <- dba.overlap(myDBA, myDBA$masks$Consensus)

myDBA.OL$onlyA

or

myDBA.OL$AandC

so I can export these subsets as .bed?

ADD COMMENTlink modified 4 months ago • written 4 months ago by corinne_hutfilz0
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