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