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(a)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.