SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Question: Advice : building transcript models using cufflinks apratap Bioinformatics 1 10-09-2012 05:33 PM
Could GSNAP results be analyzed by Cufflinks? aquleaf Bioinformatics 2 03-07-2012 09:12 AM
contigs generation via gsnap -> cufflinks Assaf Bioinformatics 0 01-18-2012 06:59 AM
NGS read mapper that would extend the seeding contig. *#1* Bioinformatics 1 10-06-2011 06:26 AM
How do I extend reads? Martiniano Bioinformatics 0 09-15-2011 04:13 AM

Reply
 
Thread Tools
Old 05-29-2012, 02:01 PM   #1
bwalts
Junior Member
 
Location: UK

Join Date: Feb 2010
Posts: 1
Default Cufflinks models from gsnap alignments extend beyond the reference

I'm using Cufflinks 2.0.0 without a reference GTF to build models from GSNAP v20120427 alignments, also made without a reference GTF (i.e. using -N 1). I noticed that some of the Cufflinks models extend beyond the end of the reference contig sequence. They also seem to extend beyond the end of the GSNAP alignments as shown in a pileup file.

For example, cufflinks reported this transcript:
Code:
scaffold02137	Cufflinks	exon	4297	4727	1000	-	.	gene_id "CUFF.17382"; transcript_id "CUFF.17382.1"; exon_number "2"; FPKM "95.5022086611"; frac "1.000000"; conf_lo "86.719816"; conf_hi "104.284601"; cov "139.246274";
But scaffold01237 is only 4696 bases long, and according to the pileup, GSNAP's alignment ends at base 4696.

Is this a known problem with this combination of Cufflinks 2.0.0 and GSNAP 20120427? I can't see how Cufflinks would know to extend the transcript if there isn't data in GSNAP's SAM/BAM output to begin with, and it makes me wonder if Cufflinks is parsing the BAM file incorrectly.
bwalts is offline   Reply With Quote
Reply

Tags
cufflinks, gsnap

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 11:33 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO