Question: Identify genes with chip signal > input prior to peak calling
gravatar for SciDuck
14 months ago by
SciDuck20 wrote:

Hi everyone,

I need to identify which genes in my histone ChIP-seq experiment have greater signal for chip than for input (enrichment). I have made an enrichment plot deepTools plotProfile, however, the profile contains negative values which I suspect are a result of regions not enriched for the histone mark of interest. This is okay but I also want to be able to plot only the regions with enrichment.

I know one way to do this would be with peak calling. But given that peak calling doesn't call all the enriched regions and since I am looking to plot the average enrichment profile of the histone mark over the all the TSS in the genome, I do not want to exclude any regions with enrichment. So I would like to find a way to identify which regions in the genome have chip signal>input and then use this for plotProfile.

Does anyone know of a way to do this besides peak calling? Please help!

ADD COMMENTlink written 14 months ago by SciDuck20

I think using clustering with plotHeatmap will yield what you want. So either --kmeans or --hclust :

ADD REPLYlink modified 14 months ago • written 14 months ago by Gautier Richard280

Thank you so much, Gautier! This is exactly what I needed. Much appreciated!

ADD REPLYlink written 14 months ago by SciDuck20

what I understood that you want to narrow down ChIPseq signal having enrichment > input (but how much 1.5 fold or 2 fold?), and then use look for enrichment near TSS. I think you need keep one thing fixed either all the TSS or ChIPseq enrichment. I would suggest to to reduce the fold change cutoff while calling peak.

ADD REPLYlink written 14 months ago by Prakash1.8k

Thank you Prakash, I will try reducing the fold change during peak calling.

ADD REPLYlink written 14 months ago by SciDuck20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1241 users visited in the last hour