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Old 04-14-2009, 11:10 PM   #5
warrenemmett
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Location: South Africa

Join Date: Nov 2008
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Quote:
Originally Posted by alim View Post
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
Hi Ali,

Thanks for the response. I have checked out TopHat which also looks like quite an interesting package. I was wondering as well about using something like 454 with ERANGE since the read lengths vary can it still be used with the ERANGE package? I am specifically concerned about the creation of splice-reads and what value to select for the splice radius, if you have any thoughts please let me know.

Thanks again!
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