Using DANPOS2 to determine nucleosome positions

[Elisheva Heilbrun]

Hello.

I want to determine the nucleosome positions from ENCODE data (ENCFF000VME).
The file is a signal file in Bigwig format - so there is no way to find the positions by just looking at the file.
I found that some people use the DANPOS2 in order to find the nucleosome positions from MNase-seq data.
However it's still unclear to me which option to use given the Bigwig format and how, and also how to verify the results.

Or maybe should I use different files in order to run the dops option?

[simon holzinger]

Hi, 

Danpos can't handle bigwig files, so you have to convert the bigwig files to wig files first. 

you can find the ucsc tool for that (bigWigToWig) at http://hgdownload.cse.ucsc.edu/admin/exe/ 

best wishes 

Simon