Question: Homer ...Software For Motif Discovery And Next Generation Sequencing Analysis
0
gravatar for Dataminer
4.1 years ago by
Dataminer2.1k
Netherlands
Dataminer2.1k wrote:

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

ADD COMMENTlink modified 3.9 years ago by Sukhdeep Singh6.0k • written 4.1 years ago by Dataminer2.1k
1

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

ADD REPLYlink written 4.1 years ago by 2184687-1231-83-4.7k

How about a link?

ADD REPLYlink written 4.1 years ago by Martin A Hansen2.8k

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

ADD REPLYlink written 4.1 years ago by Dataminer2.1k

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

ADD REPLYlink written 4.1 years ago by Pierre Lindenbaum72k

Indeed Pierre :)

ADD REPLYlink written 4.1 years ago by Dataminer2.1k

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

ADD REPLYlink written 4.1 years ago by Michael Schubert6.2k
3
gravatar for Dataminer
4.0 years ago by
Dataminer2.1k
Netherlands
Dataminer2.1k wrote:

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.

ADD COMMENTlink written 4.0 years ago by Dataminer2.1k
1
gravatar for Lars Grontved
3.8 years ago by
Lars Grontved10 wrote:

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.

ADD COMMENTlink written 3.8 years ago by Lars Grontved10

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.

ADD REPLYlink written 3.7 years ago by Curiosity120
1
gravatar for Sukhdeep Singh
3.3 years ago by
Sukhdeep Singh6.0k
Germany
Sukhdeep Singh6.0k wrote:

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

ADD COMMENTlink modified 3.2 years ago • written 3.3 years ago by Sukhdeep Singh6.0k
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