Edge, Please send questions like this to the galaxy-user mailing list, where many people see your email and can help you and/or benefit from it. I've cc'd the list for this reply. The thread you linked to is out of date. To get sequences for the features in a GTF file, you can use the 'Extract Genomic DNA' tool and set the option 'Interpret features when possible' to Yes. To get sequences for Cufflinks transcripts, use the transcripts.gtf as input to the tool. Best, J. On May 12, 2011, at 3:08 AM, Edge Edge wrote:

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

Sorry that I got a bit confusing about the explanation that you given to Karen, "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 your advice.

best regards edge Master Student UTAR Malaysia