In order to have the transcript_id for each sequence extracted from the
cuffmerge .gtf file I had to change the extract_genomic_dna.py by adding
the following lines after line 153:
attributes = gff_util.parse_gff_attributes( feature )
if ( "transcript_id" in attributes ):
name = attributes.get( "transcript_id", None )
This way the variable name gets the transcript_id if it exists.
If it's correct, I would appreciate this modification in future galaxy
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