Peak Calling For Non-Chip Data?

Question

[vedtopkar]

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?)

[dario.garvan]

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

[vedtopkar]

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

Answer 1

[Mikael Huss]

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.

[vedtopkar]

This is perfect, thanks!

Answer 2

[Ming Tommy Tang]

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

[vedtopkar]

Very helpful, thanks!