Is there an easy way to compute FPKMs from bam files (Tophat output)? I am using cuffdiff to compare 2 samples using an annotation and that gives me the FPKMs for the genes in the annotation, but is there a way to do that per sample more easily?
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Hi lpn,
Cufflinks outputs the FPKM results in the first step - the cufflinks step. Here is what the manual says:"Cufflinks produces three output files:
1) transcripts.gtf ......
2) isoforms.fpkm_tracking
This file contains the estimated isoform-level expression values in the generic FPKM Tracking Format. Note, however that as there is only one sample, the "q" format is not used.
3) genes.fpkm_tracking
This file contains the estimated gene-level expression values in the generic FPKM Tracking Format. Note, however that as there is only one sample, the "q" format is not used. "
Hope this helps.
Douglas
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