Jeremy, I think we've looked at the same threads in seqanswers! Hope this does fix the problem, pity its not explained in the cufflinks manual. Look forward to the update. Cheers David On 8 Dec 2010, at 17:04, Jeremy Goecks wrote:
David,
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.
Best, J.
On Wed, Dec 8, 2010 at 10:41 AM, David Matthews <D.A.Matthews@bristol.ac.uk> wrote: Hi,
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...
Cheers David
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.
http://seqanswers.com/forums/showthread.php?p=30942
Best, J.