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Old 02-05-2010, 09:13 AM   #1
DrD2009
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Location: Kansas City

Join Date: Oct 2009
Posts: 88
Default Bowtie and Cufflinks

Hello,

I have aligned Solexa sequencing data using Bowtie and plan on creating expression profiles using Cufflinks by looking at RPKM values.

There is one thing I am curious about. Is there a way to compare your alignments to annotated regions, so you can give the reads a name along with an RPKM value? I'm assuming Cufflinks simply gives you a read and it's RPKM, what I would like is to be able to see X gene, X miRNA, X puesdogene has an RPKM value of Y.

Is there a way to make this possible? Any suggestions would be great.


Thanks,
Brandon
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