Question: ChIPseq Peak annotation and downstream analysis
gravatar for reubenmcgregor88
2.2 years ago by
reubenmcgregor8850 wrote:

Hi all,

I know this has been asked before but not in a few years and I was wondering if there is an update.

I have some ChIPseq data and managed to get it to the stage where I am happy with the quality and mapped the reads and called peaks. However now I am looking to do some downstream analysis and rather than just looking at selected genes of interest it would be good to be able to identify significant peak location to genes to create a gene list. Is there an automated tool for this in Galaxy?

Further, is it possible to then preform some kind of gene-ontology analysis to suggest functional groups for significantly enriched genes with nearby ChIPseq peaks?

I have seen this done in some papers with pipelines in the public galaxy server like Cistrome, but several of the tools, like "ChipToPeak" are no longer working?

Sorry for the list of questions. I have little experience but will teach myself as much as I can :)


ADD COMMENTlink modified 2.2 years ago by Bjoern Gruening5.1k • written 2.2 years ago by reubenmcgregor8850
gravatar for Bjoern Gruening
2.2 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:


this really depends on the Galaxy server you are using. In general this is possible with Galaxy. Have a look at some ChIP-seq training we prepared to call peak and plot them genome wide with deepTools.

Ciao, Bjoern

ADD COMMENTlink written 2.2 years ago by Bjoern Gruening5.1k


I am using the main instance of galaxy.

I have actually used your training to get to the stage I am at. It's a great tutorial, would have been lost without it.

I've completed it and used it to map my own reads and look at the data for my "favourite" genes in IGV and it worked great.

But it's the next steps I'm stuck with. So much data, how do I get a meaningfull list of genes that have chip-seq peaks in or around their promoter and group them according to function etc. Or even motif analysis, which other TF binding motifs are there in the regions of my ChIP sew bed files etc?

Thanks so much for your help already

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by reubenmcgregor8850


that is a little bit more complicated to explain. But the essential parts are explained here:

Essentially you download a list of genes, only the coordinates and intersect them with the peaks from MACS. I hope this second tutorial will help you with this.

Ciao, Bjoern

ADD REPLYlink written 2.2 years ago by Bjoern Gruening5.1k

It's great, just as the there one was thanks,

Stupid question, in the tutorial why do you "get flanks" with an offset of 10,000bp? Surely this will only get flanks starting 10,000bp upstream of all the genes? Missing a large portion of upstream sequence that could be promote region?

Like I said maybe a stupid question...

ADD REPLYlink written 2.2 years ago by reubenmcgregor8850

I need to look it up, but I think the offset was 10.000 but the length was 12.000, so you actually have 10.000 bp of the promoter and 2.000 of the gene.

ADD REPLYlink written 2.1 years ago by Bjoern Gruening5.1k
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