David,<div><br></div><div>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&#39;s going to require a bit of time to add the necessary code to make it happen. I&#39;d guess we&#39;ll have it done in about a week.</div>

<div><br></div><div>If you want help setting things up locally, let me know and we&#39;ll make it happen.</div><div><br></div><div>Best,</div><div>J. </div><div><div><br><br><div class="gmail_quote">On Wed, Dec 8, 2010 at 10:41 AM, David Matthews <span dir="ltr">&lt;<a href="mailto:D.A.Matthews@bristol.ac.uk">D.A.Matthews@bristol.ac.uk</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word">Hi,<div><br></div><div>Thanks for trying, at least its not something I&#39;m missing which is reassuring! No response from Adam yet, I&#39;ll give him another prod...</div>

<div><br></div><div><br></div><div>Cheers</div><div>David</div><div><div></div><div class="h5"><div><br></div><div><br></div><div><br></div><div><br><div><div>On 8 Dec 2010, at 15:36, Jeremy Goecks wrote:</div><br><blockquote type="cite">

<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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.<br>




<br>
Any ideas? Do you want access to my files?<br></blockquote><div><br></div><div>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&#39;ve had no luck.</div>



<div><br></div><div>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&#39;s an open but old thread asking for a fix; I&#39;ve bumped it in hopes of getting a response.</div>



<div><br></div><div><a href="http://seqanswers.com/forums/showthread.php?p=30942" target="_blank">http://seqanswers.com/forums/showthread.php?p=30942</a></div><div><br></div><div>Best,</div><div>J.</div><div><br></div><div>

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