Thanks for sending the data link, this helped to narrow down the root
cause of the issue.
The UCSC-sourced GTF file has the attributes gene_id and transcript_id
set to the same value (both as transcript_id). The result of this is
that each transcript is interpreted by Cufflinks as a single gene, with
no gene grouping (thus no isoforms).
We have plans to develop a work-around. This would likely involve (for
the refGene track in particular) the value in the UCSC's primary table
refGene.name2 being swapped into the refGene GTF file's gene_id value.
This would generate accurate gene-level statistics when the file is used
as input to Cufflinks. You could do the same swap (outside of Galaxy) if
you wanted to give it a try and have resource.
Very sorry for the current inconvenience,
On 7/25/11 11:26 AM, Jennifer Jackson wrote:
Chromosome names must be exact between all input files). Also, the SAM
file and GTF file both must be sorted the same way. This FAQ may be of
If still a problem, please share the history with me directly either
using my email address or generate the share link and email to me
(only). Use "Options -> Share or Publish", not just your sessions
On 7/22/11 8:45 AM, Aleks Schein wrote:
> Dear all,
> I am trying to run Cufflinks installation in Galaxy on Solexa RNAseq
> samples from HeLa cells.
> Running Cuffcompare, according to the manual, should produce a tmap
> file, listing FMI values for detected isoforms. However, my files only
> have either "100" or "0" in FMI field. And FPKM column contains
> Is there something wrong with my input files, or parameter settings? Or
> is it rather a specific issue with Galaxy Cufflink's installation?
> The data in question is available here:
> Aleks Schein
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