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Old 04-21-2011, 09:38 AM   #1
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Location: New Haven

Join Date: Jun 2010
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Default Question to combine Bowtie output with Tophat's -- impact on Cufflinks FPKM values

Dear all,

I am using the latest versions of tophat (as of today) to map a non-model organism's transcriptome to a closely related model organism's genome. After trying almost all available parameters in Tophat, I was only able to get FPKM values for 170 genes (the model organism has ~17,000 genes) as cufflinks output.

This led me to do separate alignments with Bowtie and once that was fed into cufflinks, I get FPKM values for ~5,000 genes.

Now, my question is I would like to utilize the isoforms detected by Tophat, however I am not sure how to correctly calculate the FPKM values for the genes that I got reads mapped by both bowtie and tophat.

Any help is greatly appreciated. Thanks.
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