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Old 04-14-2009, 08:28 AM   #4
alim
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Location: pasadena, ca

Join Date: Jun 2008
Posts: 14
Default ERANGE for non-Illumina data

Hi Warren,

I'm sorry if I didn't get back to you by email!

I certainly don't have any explicit support for SOLiD colorspace; since we only have Illumina sequencers at Caltech, I don't even have the data and tools to support it even if I wished.

But, assuming that you could dump the reads out of colorspace into fasta/fastq, then you should be able to map the reads against a reference genome (or reference+splice junction, aka an "expanded genome") using bowtie and then proceed with the rest of ERANGE !

There are several other packages out there that are just starting to appear. TopHat is another one that has support for RPKM, etc.... As far as I know, it also needs a reference genome & start from fasta/fastq.

Ali
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