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Old 08-25-2011, 07:52 AM   #1
Junior Member
Location: Columbia, MO

Join Date: Aug 2011
Posts: 7
Default FPKM_tracking file question

I've got two questions about a Tophat alignment and Cufflinks analysis on some rat RNAseq data
1) I was wondering what an acceptable range of FPKM values should look like. I've sorted some Cufflinks jobs to retrieve a list of the genes with the most mapped fragments and the FPKM values from the genes.fpkm_tracking files seem awfully inflated, and I haven't used quantile normalization. Are we talking 0-50, 0-200,000, because I have some FPKMs that large.
2) Why do the some rows in the fpkm_tracking files have the standard 'CUFF' id and some have the gene names? I've provided annotation at every step, and every row that I've checked with the 'CUFF' id is an annotated gene.
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Old 08-25-2011, 09:59 AM   #2
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

1) As a guess, you may have rRNA or other contamination.

2) Don't know. Are you using the 'merged.gtf' file and did you use your original annotation file when merging?
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