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