Hi,

I just read through the post at the following 
link, http://lists.bx.psu.edu/pipermail/galaxy-user/2011-February/001934.html
I'm facing the same problem as well.
I'm desired to extract out the assembled transcript by Cufflink.
Can I know that how I link my output file from Tophat and Cufflink with the 
Galaxy?
I'm having the following output file right now:
junctions.bed
insertions.bed
deletions.bed
accepted_hits.bam
human_reference_genome.fasta
transcripts.gtf
isoforms.fpkm_tracking
genes.fpkm_tracking

I got a bit confusing about the explanation below:
" in order to get the sequence data for transcripts in a Cuff* GTF file, you'll 
want to select for only exons (use Galaxy's 'Extract Features' tool) and then 
use the resultant dataset as input to Extract."

Thanks a lot for advice.

best regards
edge
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