What Nucleosome Positioning Software Do You Use?

Question

[KCC]

There seems to be a large amount of software out there. Has their been any work comparing, rating or ranking different software? What do you use?

[Alastair Kerr]

Theoretical positioning or for working with NGS data?

[KCC]

NGS data. Thanks.

[Madelaine Gogol]

I'm also interested in this question. I'll be starting with this list: http://generegulation.info/index.php?option=com_content&view=article&id=29&Itemid=63

Answer 1

[Ian]

I recently saw a tweet from the Gottardo lab about their new software "Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data":

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032095

I realise this is not an informed suggestion, but i rate their work very highly, e.g. PICS for ChIP-seq analysis.

Answer 2

[Madelaine Gogol]

Old question, but I've recently tried PING 2.0 and am also trying DANPOS. Though the installation was a little hairier for DANPOS (a set of python scripts that depends on python package rpy2, which requires an oldish version of R), the method is easier for me to understand. Also works for comparison of nucleosomes in different samples, whereas PING is more designed to find nucleosomes in an individual sample.