Re: [galaxy-user] Extract sequences from [gtf file] + [genome FASTA file]

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

Re: [galaxy-user] Extract sequences from [gtf file] + [genome FASTA file]

Dinesh, Please send questions such as these to the galaxy-user mailing list (which I've cc'd). You can find the 'Extract Genomic DNA' tool under the 'Fetch Sequences' menu. You may also want to use tool search ('Options - Show Tool Search'). Thanks, J. On Wed, Mar 2, 2011 at 2:31 PM,

Re: [galaxy-user] Extract sequences from [gtf file] + [genome FASTA file]

I was thinking of something different. Here is a example of a three-exon transcript, in gtf format: contig00035 Cufflinks transcript 3 22 1000 + . gene_id CUFF.23955; transcript_id CUFF.23955.1; contig00035 Cufflinks exon 3 10 1000 + . gene_id CUFF.23955; transcript_id CUFF.23955.1;