Tool:ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.

Question

[support]

Standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data:

http://www.ncbi.nlm.nih.gov/pubmed/24735413

--Genohub

[Istvan Albert]

I don't want to discourage people from submitting tools and publications but what would work best is a little bit more context and personal experiences.

1. has the submitter tried the tool,
2. does it really do what it claims to
3. is it feasible to install it
4. why is it better than an alternative
5. etc

Answer 1

[Alex Reynolds]

Looks like a Galaxy tool to make the aggregate profiles and heatmaps we made for various transcription factors in our 2012 Nature paper.

The indexing aspect is interesting, but we may have an answer to that in the coming months that fixes some of the downsides with that style of indexing and compression.

[Chirag Nepal]

What is the name of that galaxy (specific) tool?

thanks

[Björn]

Propably deepTools: https://github.com/fidelram/deepTools/wiki

You can also find it in the Galaxy Tool Shed.

Cheers,

Bjoern