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Old 11-10-2010, 12:25 PM   #13
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Location: oxford, uk

Join Date: May 2010
Posts: 5
Default Cufflinks

I was wondering if anyone knows what the status in genes.expr and transcripts.expr (output files of Cufflinks) means? I can't find the meaning in the manual. A possible meaning is "can be one of OK (test successful), NOTEST (not enough alignments for testing), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents testing", but this is actually the description of "test status" which is a column in the Cuffdiff output files.

What shall I do with genes (or transcripts) whose status is FAIL? Shall I assume that their FPKM is 0 or take the FPKM of these genes regardless of their status?

Cufflinks v0.9.1b was used in my experiments, but the problem of getting multiple FPKM for some genes still exists. Running Cufflinks without a GTF file seems to solve this problem, but then I don't know how to link the FPKM to the corresponding Ensembl ID. If I provide a GTF file when running Cufflinks, I'll get multiple FPKM and FAIL status for some genes.

What shall I do with genes that have multiple FPKM? Shall I add the FPKM together or choose only the FPKM that matches the start and end position of these genes?

Thank you very much for your time.

Last edited by yjlui; 11-11-2010 at 06:53 AM.
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