On Sat, Dec 14, 2013 at 8:52 AM, Jorge Braun <braun_...@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
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