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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