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Old 08-06-2011, 07:56 PM   #1
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Location: United States

Join Date: Aug 2011
Posts: 2
Default FPKM determination of de novo transcripts

I've used a de novo assembler on some pe rna seq data. However, I'd like to determine the FPKM of the transcripts that have been assembled. I've mapped the reads using bowtie. However, is there a way to get Cufflinks to use these alignments and the library of assembled transcripts to determine the FPKM?
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bowtie, cufflinks, denovo, denovo assembly, fpkm

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