DEXseq alternative splicing detection
1
0
Entering edit mode
7.0 years ago
xd_d ▴ 110

Hello all,

I know with DEXseq i get the differential usage of exon accross samples. I read in some papers that they detect 5'/3' alternative splicing events, but they dont say how they do that.

Do anybody know how i get these events from a DEXseq workflow output ?

RNA-Seq • 2.4k views
ADD COMMENT
0
Entering edit mode

what is your aim? what is the difference between the question you are asking now and the question you asked before?

ADD REPLY
0
Entering edit mode
7.0 years ago

I think they take the 5'/3' difference and test that as a separate exon. In other words they split an exon into two smaller sub-exons and testing each of them separately. Do however note that this only works for quite large changes as you need reads (30-100nt) that maps uniquely to the regions you test against.

If you want to find smaller features a better approach is to predict these changes from transcript/isoform level data. You can use cufflinks/cuffdiff to quantify and predict isoform switches and afterwards use tools such as spliceR (which directly supports cufflinks/cuffdiff data) to analyze all 6 types of alternative splicing.

ADD COMMENT

Login before adding your answer.

Traffic: 1657 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