SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
[DEXSeq] exon counts to "PSI" (exon inclusion level) yerbol Bioinformatics 3 11-23-2015 05:32 PM
DEXSeq: How to get expresion value for each exon? fabrice RNA Sequencing 0 05-24-2015 01:46 AM
DEXSeq error: 'SAM optional field tag NH not found' Kwangwoo Bioinformatics 5 08-29-2014 01:36 AM
DEXseq: different usage for the shared exon capricy Bioinformatics 1 02-03-2014 04:36 AM
DEXSeq: dexseq_count.py produces lots of warnings (mate could not be found) enomis Bioinformatics 15 11-08-2013 01:48 PM

Reply
 
Thread Tools
Old 11-24-2015, 06:27 AM   #1
ebe
Junior Member
 
Location: France

Join Date: Apr 2013
Posts: 6
Default DEXseq : a known DE exon not found

Hi,

We focus on alternative splicing for one gene (with many exons).
We test several statistical methods (EdgeR, DESeq, DEXSeq) to identify DE exons, and we also calculate the PSI values with the IPSA package.

We know some exons as DE according to some biological experiments (in our lab + bibliography). We find some of them with the EdgeR or DESeq methods.
When we apply DEXseq method to our samples (4 samples x 2 conditions), we easily find a exon known as DE, but not a second exon (found as statisticaly DE with EdgeR and DESeq, and significant distinct PSI according to experimental conditions).
Why?

context :
Reads are single-end, 700nt length (454 sequencing), it's a targeted RNAseq (PCR baits in the 5' and 3'UTR of the gene).
The second exon not found is the penultimate exon..

Could anybody help us, please?
Thanks!
ebe is offline   Reply With Quote
Reply

Tags
alternative splicingage, dexseq, differential exon usage, exon, rna seq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO