Question: Peak Calling For Non-Chip Data?
1
gravatar for vedtopkar
5.7 years ago by
vedtopkar60
vedtopkar60 wrote:

I want to call peaks for a nucleosome density signal from the ENCODE dataset. Is it ok to use a package like MACS to do so, or are there underlying assumptions to such packages that I am overlooking?

Thanks!

EDIT: Upon further inspection, the data I want to call peaks for is in the .bigWig file format. Any way to call peaks on such a format? (i.e. converting it to a .bed file?)

macs encode peak-calling • 2.0k views
ADD COMMENTlink modified 5.7 years ago by Ming Tang2.4k • written 5.7 years ago by vedtopkar60

Why don't you want to use ENCODE's peak calls ?

ADD REPLYlink written 5.7 years ago by dario.garvan440

As far as I can tell, peak calls are not published for the Nucleosome position dataset. (I'd love to be proven wrong, however!)

ADD REPLYlink written 5.7 years ago by vedtopkar60
1
gravatar for Mikael Huss
5.7 years ago by
Mikael Huss4.6k
Stockholm
Mikael Huss4.6k wrote:

I'd take a look at this very recent publication (http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2596.html) which I haven't tried yet but am about to do.

ADD COMMENTlink written 5.7 years ago by Mikael Huss4.6k

This is perfect, thanks!

ADD REPLYlink written 5.7 years ago by vedtopkar60
1
gravatar for Ming Tang
5.7 years ago by
Ming Tang2.4k
Houston/MD Anderson Cancer Center
Ming Tang2.4k wrote:

check if the ones below are what you are looking for

http://code.google.com/p/danpos/ http://code.google.com/p/dantools/

Bioconductor packages http://bioconductor.org/packages/release/bioc/html/nucleR.html http://bioconductor.org/packages/release/bioc/html/PING.html

ADD COMMENTlink written 5.7 years ago by Ming Tang2.4k

Very helpful, thanks!

ADD REPLYlink written 5.7 years ago by vedtopkar60
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