Question: How can I make RSEM to align ChIPseq signal to the nearest gene?
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gravatar for moushengxu
10 months ago by
moushengxu310
moushengxu310 wrote:

I guess I can make a GTF by myself, and let the GTF associate genomic coordinates with genes. But assigning coordinates to closest genes is not a simple task. Overlapping gene regions can be problematic. Is there such a GTF available or is there an option to turn on/off with rsem-prepare-reference/rsem-calculate-expression/etc.?

Thanks in advance.

ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 10 months ago by moushengxu310

What is your end goal with all of this?

ADD REPLYlink written 10 months ago by Devon Ryan82k

Good question.

Assign ChIP signals to genes.

ADD REPLYlink written 10 months ago by moushengxu310
1
gravatar for Devon Ryan
10 months ago by
Devon Ryan82k
Freiburg, Germany
Devon Ryan82k wrote:

Exactly what kind of signal? I presume you either want to assign peaks to genes (bedtools closest) or look at signal distributions near genes (see computeMatrix and plotHeatmap from deepTools).

ADD COMMENTlink written 10 months ago by Devon Ryan82k

Could be Pol2, Histone modifications, ATAC, etc.

For Pol2, usually we would be interested in +-5k from TSS; for histone modifications, ATAC, double strand breaks, ... , often you want to check the whole genome regardless how far/close the signal is to a gene.

ADD REPLYlink written 10 months ago by moushengxu310

Then you want computeMatrix from deepTools followed by either plotProfile or plotHeatmap.

ADD REPLYlink written 10 months ago by Devon Ryan82k
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