Hi,

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[8] )

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 distributions.

Thanks!

Adhemar