Hi Aleks,

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,

Best,

Jen
Galaxy team

On 7/25/11 11:26 AM, Jennifer Jackson wrote:
Hello Aleks,

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
interest:
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq

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
browser URL.

Best,

Jen
Galaxy team

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 only
zeros.
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:
http://main.g2.bx.psu.edu/u/aleks/h/guided-assemblyadvanced

Thanks,

Aleks Schein



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