Hello Christopher,

We did some testing here using your available data and are fairly certain that the problem is with the tool itself and not the Galaxy wrapper. Contacting the author and asking about the issue is probably the best way forward. If you have time, we would be glad to learn about the outcome.


Best,

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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