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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--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
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use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
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please use the interface at:
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