Hi, I sent the following question to the bioconductor list and they suggested I posted it here to get a fuller answer.
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. Additional note: I have both the raw sequence files and the insert sequence files (sequenced bases between the two adapters) Many Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: [email protected] ************************************************************** 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. This e-mail message is confidential and for use by the a...{{dropped:2}} _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
