On Sat, Dec 14, 2013 at 8:52 AM, Jorge Braun <[email protected]> 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
