[BioC] Solexa fastq files and BLAT

Daniel Brewer daniel.brewer at icr.ac.uk
Tue Jan 13 12:35:35 CET 2009


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.



Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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