Homer ...Software For Motif Discovery And Next Generation Sequencing Analysis

Question

[Dataminer]

Hi!

I just came across this software suite HOMER , it seems to be quite good.

I would like to have an opinion on this software from the people who are working with NGS data analysis (specially with ChIP Seq and with RNA seq data analysis) and where they rank it in comparison with other softwares (GREAT, completeMotifs etc).

Thank you

[2184687-1231-83-]

This looks like a very interesting toolkit. Thanks for bringing it up.

[Martin A Hansen]

How about a link?

[Dataminer]

http://biowhat.ucsd.edu/homer/download.html

[Pierre Lindenbaum]

Nice logo :-) http://biowhat.ucsd.edu/homer/pic2.gif

[Dataminer]

Indeed Pierre :)

[Michael Schubert]

Have you seen the one at the bottom as well? ;-) http://biowhat.ucsd.edu/homer/pic1.jpg

Answer 1

[Dataminer]

My advice will be, ' Stick to R and Bioconductors" and rest of the tools for ChIP seq analysis could be used for extended analysis.

Note: Since no one answered, so I thought of writing down few lines. Which could help any new comer in ChIPseq analysis field. HOMER is not extra ordinary, just normal.

Answer 2

[Lars Grontved]

I have used Homer for ChIP-seq analysis and can highly recommend it. The program offers analysis of ChIP-seq data from A-Z. I especially like the de novo motif analysis part and related tools.

[Curiosity]

Homer also producing different results all the time and have lot f bugs in quality control step for RNA-Seq data. Watch out for these.

Answer 3

[Sukhi Singh]

I like Homer. Mostly, I use a collection of different tools for the various parts of the ChIP-Seq analysis.

Another one I would recommend to have a look on is the 'pyicos'

Cheers