Question: Annotation Histone Modification ChIP-seq
gravatar for mads_ks
23 months ago by
mads_ks0 wrote:

Hi there,

I am new to this and have used MACS for peak calling and I now want to annotate the peaks. I am not sure which tool I should be using for this. I performed ChIP to investigate histone modifications looking at HDAC1 and 2. In theory I think I should be finding peaks (or lack of peaks) at the promoter regions of genes. I have used rat tissue. I have downloaded the rat UCSC file but I am not sure what to do next?

The second part of my question is that I want to compare regulated regions between samples, I have 2 treatments and a control sample and want to see which genes are more or less regulated by HDAC1 and 2 in these samples. What tool should I be using to compare between them all?

Thanks for your help,


chip-seq • 766 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 23 months ago by mads_ks0
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The public Cistrome Galaxy server has many custom tools with a specific focus on ChIP-chip/seq data.

Hopefully this helps! Jen, Galaxy team

ADD COMMENTlink modified 22 months ago • written 22 months ago by Jennifer Hillman Jackson25k

Thanks Jen,

I am trying to use the tools on Cistrome but having a little trouble... The BETA-minus tool is what I want to use but it won't let me add a reference genome, which I need to do. It is strange because the instructions for the parameters say to do this... Am I doing something wrong? I have downloaded my reference genome from UCSC


ADD REPLYlink written 19 months ago by mads_ks0
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