Is there a tool to find if the gene ends are covered by RNAseq reads?

capricy · 03-06-2015, 01:34 PM

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

Brian Bushnell · 03-06-2015, 02:07 PM

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.

Michael.Ante · 03-09-2015, 02:36 AM

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

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03-06-2015, 01:34 PM	#1
capricy Senior Member Location: 63130 Join Date: Apr 2012 Posts: 125	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

03-06-2015, 02:07 PM	#2
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	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.

03-09-2015, 02:36 AM	#3
Michael.Ante Senior Member Location: Vienna Join Date: Oct 2011 Posts: 123	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