[BioC] Aligned RNA-seq data to ranked list of genes

[Thomas Girke]

Also, you may want to take a look at the Vignette of the
GenomicRanges package: 
http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html

The package is particularly useful if you aligned your reads against a genomic
reference. A very short code sample is given here:
http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-RNA-Seq-Analysis

If you aligned your reads against a transcriptome reference then things
are even easier. All you need is the ShortRead package. A short use case
is available here:
http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-RNA-Seq-Profiling-Exercise

Thomas


On Thu, May 27, 2010 at 06:14:03PM +0200, Wolfgang Huber wrote:
> Paul
> 
> a relatively lightweight and reasonably fast possibility is described 
> here: http://www-huber.embl.de/users/anders/HTSeq/doc/tour.html#tour
> 
> 	Best wishes
> 	Wolfgang
> 
> 
> 
> Kasper Daniel Hansen scripsit 25/05/10 18:26:
> >One possibility is Genominator which uses an SQLite backend for
> >storing the data and does require a bit of time in setting up the
> >data, but you can also do a pipeline entirely in R using
> >IRanges/GenomicRanges and ShortRead.
> >
> >Kasper
> >
> >On Tue, May 25, 2010 at 11:22 AM,<paulig2001 at yahoo.co.uk>  wrote:
> >>Hello,
> >>
> >>I've got aligned rna-seq data (aligned using MAQ) for a sample and want 
> >>to turn it into a list of genes ranked by their expression level in that 
> >>sample. I'm wondering if anybody can point me towards a tutorial or a 
> >>package that would allow me to do this?
> >>
> >>Thanks a bunch.
> >>
> >>Paul
> >>
> >>
> >>
> >>
> >>        [[alternative HTML version deleted]]
> >>
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> 
> -- 
> 
> 
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
> 
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