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Old 05-03-2012, 12:06 AM   #3
sdriscoll
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Location: San Diego, CA, USA

Join Date: Sep 2009
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You might try one of the "no genome" assemblers like Trinity or Abyss to build a "gene" library from your data. I think those put together some consensus set of sequences assembled from your reads. The you could build a bowtie reference from those FASTA sequences and align your reads to it with bowtie. Finally you can count reads aligned to each one and compare samples using something like DESeq.

You'll need some major computer power to run Trinity, from what I hear. That process of assembling sequences from reads is much more reasource consuming than the bowtie alignment stage.
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