Question: Cuffmerge Loses P_Id
0
Christopher M. Weber • 30 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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modified 6.5 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
6.5 years ago by
Christopher M. Weber • 30
