Turns out the problem is that cuffcompare requires the -s option to be present (as well as necessary sequence files) in order for p_id attributes to be generated in the combined transcripts file. This is definitely doable in Galaxy, but it's going to require a bit of time to add the necessary code to make it happen. I'd guess we'll have it done in about a week.

If you want help setting things up locally, let me know and we'll make it happen.


On Wed, Dec 8, 2010 at 10:41 AM, David Matthews <D.A.Matthews@bristol.ac.uk> wrote:

Thanks for trying, at least its not something I'm missing which is reassuring! No response from Adam yet, I'll give him another prod...


On 8 Dec 2010, at 15:36, Jeremy Goecks wrote:

In each case, after running t0 and t8 in cuffcompare to generate a combined gtf I used that one to run cuffdiff. Everytime, the CDS files are empty and no p_ids can be found anywhere (in any of the gtf files). This is driving me mad!! I do not use a reference gtf for cufflinks (because that would restrict the analysis to known genes only) is that where I am going wrong? ON the other hand all the other things are filled out (e.g. splicing diff) and they seem - on the face of it - accurate.

Any ideas? Do you want access to my files?

After writing you back yesterday, I reran some Cufflinks and Cuffcompare analyses to see if I could generate a GTF file with both tss_id and p_id. Like you, I've had no luck.

I expect this is a bug in Cuffcompare and something that Adam can best address. Have you heard back from him? Looking on seqanswers, there's an open but old thread asking for a fix; I've bumped it in hopes of getting a response.