Default strand of mutations
0
0
Entering edit mode
5.1 years ago
Gene_MMP8 ▴ 240

I have downloaded 10000 SNVs from the COSMIC database. These are all cancer-causing variants. Each of these mutations has strand information attached to them. The problem is every mutation has been flagged as belonging to the plus strand. Why is that? Is it a convention? To give you an example, consider this mutation COSM1099572. It is listed as a plus-strand mutation (G>A) if you download the database and view it in R. But when I click on the ensemble contig information, the base on the plus strand is C and on the minus strand is G. My question is, is there a convention to consider everything on the plus strand?

genome • 780 views
ADD COMMENT
0
Entering edit mode

Why is that? Is it a convention

Yes, convention is to refer to the top strand.

ADD REPLY

Login before adding your answer.

Traffic: 2521 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6