useq-users

[Useq-users] RNA-seq data - Identification of enriched regions

[Myrto K. <kos...@gm...>]

Hi,
I have RNA-seq data (76bp paired-end) of a single cell type and would like
to identify regions that are transcribed but are not annotated (e.g. novel
exons).

My alignments are in BAM format and come from GSNAP.

Can I perform such analysis using USeq?

Any help would be much appreciated.

Thanks,
M

-- 
Myrto Areti Kostadima
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
UK

Re: [Useq-users] RNA-seq data - Identification of enriched regions

[David N. <dav...@gm...>]

So no control sample?  You can convert to PointData and run the
DefinedRegionScanSeqs and ScanSeqs with just one sample to get read counts
but there are no confidence calls made here.  See
http://useq.sourceforge.net/usage.html

-cheers, D

From:  Myrto Kostadima <kos...@gm...>
Date:  Mon, 24 Oct 2011 17:10:36 +0100
To:  <use...@li...>
Subject:  [Useq-users] RNA-seq data - Identification of enriched regions

Hi,
I have RNA-seq data (76bp paired-end) of a single cell type and would like
to identify regions that are transcribed but are not annotated (e.g. novel
exons).

My alignments are in BAM format and come from GSNAP.

Can I perform such analysis using USeq?

Any help would be much appreciated.

Thanks,
M

-- 
Myrto Areti Kostadima
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
UK
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