Question: How can I make RSEM to align ChIPseq signal to the nearest gene?
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gravatar for moxu
2.3 years ago by
moxu440
moxu440 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 21 months ago by Biostar ♦♦ 20 • written 2.3 years ago by moxu440

What is your end goal with all of this?

ADD REPLYlink written 2.3 years ago by Devon Ryan93k

Good question.

Assign ChIP signals to genes.

ADD REPLYlink written 2.3 years ago by moxu440
1
gravatar for Devon Ryan
2.3 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k 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 2.3 years ago by Devon Ryan93k

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 2.3 years ago by moxu440

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

ADD REPLYlink written 2.3 years ago by Devon Ryan93k
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