Hello Christopher,

I see that this was also posted at SeqAnswers yesterday. I searched and didn't see anything specifically in the manual or at seqanswers that addresses this (but if someone else can find it, please add to this thread):
http://seqanswers.com/forums/showthread.php?t=20084

Do you think this is a problem with the Cuffmerge program itself? If so, going to the authors is the next step by emailing tophat.cufflinks@gmail.com
http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results
(See: Example: unexpected results with RNA-seq analysis tools.)

If you think this is a problem may be with the Galaxy wrapper around CuffMerge, we can take a closer look. Please share a link to your history containing this data. Use "Options (top 'gear' icon  in history panel) -> Share or publish", generate a share link, copy link, and email link back directly to me. Note the dataset #'s involved and leave all datasets unhidden/undeleted.

Thanks!

Jen
Galaxy team

On 5/15/12 1:38 PM, Christopher M. Weber wrote:
Hello,

Problem: Cuffmerge loses p_id from reference genome in merged gtf file on Galaxy online server resulting in blank cds cuffdiff files.

DATA Input to Cuffmerge or Cuffcompare:
Two fly cufflinks transcript assemblies created from bam files in Galaxy server using reference annotation and bias correction.

Options:
Use Reference Annotation:  YES
UCSC DM3 genes gtf (D. melanogaster) or ENSMBL 5.25 genes gtf

Use Sequence Data: YES

Result:  tss_id found in cuffmerge but no p_id with either reference annotation file.  Examples included below.

Reference:
2L protein_coding stop_codon 8608 8610 . + 0 exon_number "2"; gene_id "FBgn0031208"; gene_name "CG11023"; p_id "P13746"; transcript_id "FBtr0300689"; transcript_name "CG11023-RB"; tss_id "TSS8369";

Cuffmerge:
Cufflinks exon 8193 9484 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "CG11023"; oId "FBtr0300689"; nearest_ref "FBtr0300689"; class_code "="; tss_id "TSS1";
2L Cufflinks exon 66721 67003 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "dbr"; oId "CUFF.1.1"; nearest_ref "FBtr0078100"; class_code "j"; tss_id "TSS2";

Help is much appreciated,

Thanks! 



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