Question: HOMER motif search, conservation and correlate ChIP-seq to RNA-seq
0
gravatar for mdp07vm
3.1 years ago by
mdp07vm20
United States
mdp07vm20 wrote:

Hi there,

I need help or advice in the following questions which may not be related to each other but are all important for the analyses that I'm currently working on. I'm analyzing my ATAC-seq and ChIP-seq data as well as correlating them to my RNA-seq data. 

1) When I use HOMER annotatePeaks.pl or findMotifGenome.pl) to search for the occurrence of my motif of interest in 3 peak files generated from 3 biological replicates, I found that in the positive control sites (that showed peak enrichment in all 3 libraries) showed up only in 1 library and not the other two despite similar enrichments in all 3 libraries at the same site. A check with other expected sites showed the same as well (some in 2 libraries and not the other). It seems like HOMER 'randomly' selected sites that showed enrichment in that motif in the 3 libraries and did not report all enriched sites like it's supposed to. 

2) I would like to correlate enriched peaks (ATAC-seq or ChIP-seq) to my RNA-seq data i.e. correlate enriched peaks to  expressed genes/TSS.

3) How do I add in conservation as a filter to enriched sites containing my motif of interest (in HOMER or other recommended programs)?

Would appreciate any help or advice given for the above questions. Thanks a million!

Thanks,

Victor

rna-seq chip-seq • 3.5k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by mdp07vm20
0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Are you using this tool in Galaxy? On a cloud or public server? This repo? https://toolshed.g2.bx.psu.edu/view/kevyin/homer

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson24k
0
gravatar for mdp07vm
3.1 years ago by
mdp07vm20
United States
mdp07vm20 wrote:

Hi Jen, no i'm not using this tool on Galaxy. I'm using it on my computer. Is there a tool (or tools) on Galaxy that can help accomplish my workflow above? Thanks.

ADD COMMENTlink written 3.1 years ago by mdp07vm20

Hi,

The link above is for a wrapped version of Homer. You will need to use this in a local or cloud Galaxy. For other analyses, there are a few tools to pick from for comparing data, including conversation data (MAF alignments). 

Galaxy server choices: http://wiki.galaxyproject.org/DevNewsBriefs

For some tutorials to help get oriented, please see:
Galaxy Main: http://usegalaxy.org -> Shared Data: Published Pages/Workflows
Galaxy wiki: http://galaxyproject.org -> Learn, Train
Videos: http://vimeo.com/galaxyproject

Best, Jen, Galaxy team

ADD REPLYlink written 3.1 years ago by Jennifer Hillman Jackson24k

Thanks Jennifer for the link. I'm a Biostar user but I wasn't aware that HOMER is available - hence, my use of HOMER on my own system. Are you able to advice on the rest of the questions i.e. 2 and 3?

Thanks,

Victor

ADD REPLYlink written 3.1 years ago by mdp07vm20
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