SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNAseq: Underrepresented RNA ends biochembug Illumina/Solexa 0 02-23-2015 11:53 AM
Tool to find reads bridging two scaffolds? illinu Bioinformatics 0 02-23-2015 06:24 AM
how to find correlation between a gene and a set of genes from one replicate RNASEQ angel-sakura Bioinformatics 0 12-21-2014 07:52 PM
How to find covered regions from bam file frewise RNA Sequencing 1 03-11-2014 01:48 AM
RNAseq analysis by DESeq : can't find a gene previously published as important elipsoid RNA Sequencing 7 10-31-2013 08:18 PM

Reply
 
Thread Tools
Old 03-06-2015, 12:34 PM   #1
capricy
Senior Member
 
Location: 63130

Join Date: Apr 2012
Posts: 125
Default Is there a tool to find if the gene ends are covered by RNAseq reads?

Hello, there,

I have tophat mapped file and the reference gff file. I wonder if there is an easy tool I can used to find if the gene ends(5'- and 3'-end) are covered by reads...

Thank you for any input!!!

Capricy
capricy is offline   Reply With Quote
Old 03-06-2015, 01:07 PM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

BBTools has a pileup utility which covers that usage:
pileup.sh in=mapped.sam normcov=normcoverage.txt normb=20 stats=stats.txt

That will generate coverage per transcript, with 20 lines per transcript, each line showing the coverage for that fraction of the transcript. "stats" will contain other information like the fraction of bases in each transcript that was covered. There are various other output options but I think those are the most relevant for you.
Brian Bushnell is offline   Reply With Quote
Old 03-09-2015, 01:36 AM   #3
Michael.Ante
Senior Member
 
Location: Vienna

Join Date: Oct 2011
Posts: 121
Default

Hi Capricy,

you might have a look at RSEQC. You just need to get your reference as a bed file (downloading is in most cases easier).
But beware of the fact, that these are just cumulative and thus smoothing plots, looking at single genes gives often a different picture.
With RSeQC's read-distribution you get some statistics about number of "tags" per 5' and 3' UTR exons.

If you want to have a deeper insight, use the UCSC table browser to get only the 5' and 3' exons and run HTSeq-count on it.

Cheers,

Michael
Michael.Ante is offline   Reply With Quote
Reply

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 09:07 PM.


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