Question: How to find polyA sites from gtf/gff?
1
gravatar for goodez
20 months ago by
goodez470
United States
goodez470 wrote:

I need a list of polyA site positions. For instance, I extracted TSS positions from a gtf file by taking the starting position of all transcript features. Would the end position of the transcript be the polyA site?

gene genome • 686 views
ADD COMMENTlink modified 20 months ago by Friederike5.2k • written 20 months ago by goodez470
2
gravatar for Friederike
20 months ago by
Friederike5.2k
United States
Friederike5.2k wrote:

Many gtf files contain the coordinates for the 3'UTR, too (check the 3rd column). Its end coordinate might be a suitable proxy.

ADD COMMENTlink written 20 months ago by Friederike5.2k
3
gravatar for Devon Ryan
20 months ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

Poly-A sites aren't typically annotated, since they often don't exist in the genome, but are rather post-transcriptionally added. See, for example wikipedia for an overview.

ADD COMMENTlink written 20 months ago by Devon Ryan93k
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