Nucleosome Peak Callers

Question

[Sinji]

Does anyone have some information regarding nuclesome peak callers for MNase-seq data?

The two options I have found are DANPOS2 and iNPS.

Unfortunately DANPOS2 relies on a extremely old version of samtools (< samtools v 1.0) and iNPS continually hangs on large data.

[biostart]

See here, it lists and compares many nucleosome callers http://bib.oxfordjournals.org/content/17/5/745

[Sinji]

What an excellent resource thank you.

Answer 1

[Carlo Yague]

I have used DANPOS in the past and I'm quite happy with it. It is reasonably fast and outputs both peak tables and bigwig files. I also enjoyed reading the original DANPOS paper.

Never tried iNPS though.

[Sinji]

Unfortunately DANPOS relies on an extremely old samtools version, while fine for quick manual peak calling, makes it unsuitable for integration into a pipeline meant for multiple different systems. It's just another dependency i'd have to add.

[Carlo Yague]

I had the old samtools problem too.

What I did was to install the old samtools version without adding it to my PATH so there was no interference with the newer samtools version already installed. Then I modified the python code to replace the samtools commands by the absolute path the old samtools. It was not too much trouble in my case.