Re: [galaxy-user] p_ids and cufflinks

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.