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What Nucleosome Positioning Software Do You Use?

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?

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updated by Ian Ian • written by KCC KCC

Theoretical positioning or for working with NGS data?

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written by Alastair Kerr Alastair Kerr

NGS data. Thanks.

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written by KCC KCC

2 answers

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.

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updated by Ram Ram • written by Ian Ian

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.

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updated by Ram Ram • written by Madelaine Gogol Madelaine Gogol

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