It appear that you are now using Ensembl make suer it is properly formated-
Chr is added to first column. It may be worth checking.
Vasu
--- On Tue, 7/19/11, Jennifer Jackson wrote:
From: Jennifer Jackson
Subject: Re: [galaxy-user] Cufflinks reporting FPKM values of all zeroes (0)
To
Hello David,
There is most likely some mismatch between the input data. Some things
to check:
First, double check that the identifiers in the reference genome exactly
match those in the RefGene gtf file and modify if necessary.
Second, make certain that your RefGene file is sorted the same
Hello!
I have come across a problem where Cufflinks is reporting all
FPKM values as zeroes (0). I have a unique RNA-Seq project from a collaborator
where they are studying eyesight by using tree shrews. I found that Ensembl
(http://useast.ensembl.org/Tupaia_belangeri/Info/Index
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