On Tue, Jan 13, 2009 at 6:35 AM, Daniel Brewer <daniel.brewer@icr.ac.uk>wrote:

> Hi,
>
> I have got hold of some solexa results in fastq format from some cancer
> mRNA samples and I would like to analyse these to look at a number of
> things.  I would like to be able to list the sequences that occur most
> often and then BLAT them against the human genome to see whether that
> sequence does occur and if so, is associated with a known transcript.
> Further down the line I would like to do some comparisons between normal
> and tumour tissue.
>
> >From looking around it seems that Shortread (in the development version)
> can be used to read in the files into BioStrings objects and then
> BSgenome can be used to perform some sort of BLAT.  Am I on the right
> lines here?
>
> Can anyone add to what packages I should be looking at and what
> approaches or techniques I should be using.
>

The Bio-sig-seq list is, perhaps the best place to ask for more details.
The shortreads package combined with the Biostrings package (for doing
alignments) is one possibility.  Also, it is possible to do the alignments
outside of R using algorithms like Bowtie, MAQ, or ELAND and the shortreads
package can read those results directly.

Sean

	[[alternative HTML version deleted]]

