On Sat, Dec 14, 2013 at 8:52 AM, Jorge Braun <braun_bio@hotmail.com> wrote:
Hello, of course, Jennifer is right for the first question . For the second question about blast ... I wonder if running after blast in galaxy I can remove sequences that can contaminate the data. It's possible?
The BLAST suite is not available on the public Galaxy server at http://usegalaxy.org but is available from the Galaxy Tool Shed if you have a local Galaxy instance: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ One way to filter your FASTA file based on BLAST hits would be to use the tabular output from BLAST with this sequence filtering tool: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id e.g. If you want to remove transcripts which seem to be mitochondria, you could BLAST against a mitochondrial database, and take only the sequence with no hits. Regards, Peter