SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
find ORFs for cufflinks assembled transcripts jiexiong Bioinformatics 1 05-08-2014 12:26 PM
Tophat: find junction spanning reads thurisaz RNA Sequencing 4 11-14-2011 04:23 AM
does tophat rescue PE reads that do not map by aligning a single end of the PE? zorph Bioinformatics 0 09-09-2011 02:14 PM
TopHat & Cufflinks failing to assemble full length transcripts jlhaner Bioinformatics 3 10-13-2010 10:46 AM
How to use short reads to find transcripts and non-coding RNA chengeng Bioinformatics 1 07-31-2009 12:40 AM

Reply
 
Thread Tools
Old 07-07-2011, 01:42 AM   #1
janec
Junior Member
 
Location: Scotland

Join Date: Jun 2011
Posts: 3
Default Reads map in Tophat, but Cufflinks doesn't find transcripts

I'm trying to analyse some RNA-seq data for the first time. We are looking for novel non-coding transcripts that are expected to (mostly) be unspliced of low abundance.

With that in mind I've managed to set up Cufflinks so it accurately reports some of the known transcripts from our region of interest, but it fails to report transcripts for adjacent sites which also have reads mapping to them, sometimes at apparently higher coverage.

I've been running cufflinks with the parameters:
-F 0 -j 0 --min_intron_lgth 1 --min-frags-per-transfrags 1

Any input into this would be most welcome, as I would like to report back to my colleagues asap.
janec is offline   Reply With Quote
Reply

Tags
cufflinks, non coding, 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 06:00 PM.


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