Question: How can I make RSEM to align ChIPseq signal to the nearest gene?
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gravatar for moushengxu
13 months ago by
moushengxu350
moushengxu350 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 6 months ago by Biostar ♦♦ 20 • written 13 months ago by moushengxu350

What is your end goal with all of this?

ADD REPLYlink written 13 months ago by Devon Ryan86k

Good question.

Assign ChIP signals to genes.

ADD REPLYlink written 13 months ago by moushengxu350
1
gravatar for Devon Ryan
13 months ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k 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 13 months ago by Devon Ryan86k

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 13 months ago by moushengxu350

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

ADD REPLYlink written 13 months ago by Devon Ryan86k
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