Question: How can I make RSEM to align ChIPseq signal to the nearest gene?
0
gravatar for moushengxu
7 months ago by
moushengxu300
moushengxu300 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 days ago by Biostar ♦♦ 20 • written 7 months ago by moushengxu300

What is your end goal with all of this?

ADD REPLYlink written 7 months ago by Devon Ryan79k

Good question.

Assign ChIP signals to genes.

ADD REPLYlink written 7 months ago by moushengxu300
1
gravatar for Devon Ryan
7 months ago by
Devon Ryan79k
Freiburg, Germany
Devon Ryan79k 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 7 months ago by Devon Ryan79k

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 7 months ago by moushengxu300

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

ADD REPLYlink written 7 months ago by Devon Ryan79k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 913 users visited in the last hour