Question: What Nucleosome Positioning Software Do You Use?
4
gravatar for KCC
7.8 years ago by
KCC4.0k
Cambridge, MA
KCC4.0k wrote:

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?

• 1.8k views
ADD COMMENTlink written 7.8 years ago by KCC4.0k
1

Theoretical positioning or for working with NGS data?

ADD REPLYlink written 7.8 years ago by Alastair Kerr5.2k

NGS data. Thanks.

ADD REPLYlink written 7.8 years ago by KCC4.0k

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

ADD REPLYlink written 6.2 years ago by Madelaine Gogol5.1k
0
gravatar for Ian
7.7 years ago by
Ian5.6k
University of Manchester, UK
Ian5.6k wrote:

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.

ADD COMMENTlink modified 11 weeks ago by RamRS25k • written 7.7 years ago by Ian5.6k
0
gravatar for Madelaine Gogol
5.7 years ago by
Madelaine Gogol5.1k
Kansas City
Madelaine Gogol5.1k wrote:

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.

 

ADD COMMENTlink written 5.7 years ago by Madelaine Gogol5.1k
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