How can I make RSEM to align ChIPseq signal to the nearest gene?

Question

[moxu]

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.

[Devon Ryan]

What is your end goal with all of this?

[moxu]

Good question.

Assign ChIP signals to genes.

Answer 1

[Devon Ryan]

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).

[moxu]

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.

[Devon Ryan]

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