Hello,
By no annotation, do you mean species-specific annotation (GTF) was not
used? And you want to compare to a protein database like Genbank NR or
RefSeq? Then these are the instructions. Please let us know if you had
something else in mind.
The sequence extraction can be done on Galaxy Main (if that is where you
are working), but the BLAST will need to be run on a local or cloud
install. To get set up (instance and data), start here:
http://getgalaxy.org
http://usegalaxy.org/cloud
The BLAST+ wrapper recently moved from the distribution to the Tool
Shed, but there are installation tools integrated to help get this into
your instance. See the latest News Brief for details (Sept 7, 2012) -
these are also good to follow as you maintain your instance:
http://wiki.g2.bx.psu.edu/News
http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_07
Questions about local/cloud installs are best directed to the
[email protected] mailing list:
http://wiki.g2.bx.psu.edu/Mailing%20Lists
To extract the transcript sequences, use the tool 'Fetch Sequences ->
Extract Genomic DNA'. This will accept a custom reference genome from
the history, if you have been using one, by changing the option "Source
for Genomic Data:" to "History".
Hopefully this helps,
Jen
Galaxy team
On 9/13/12 10:09 AM, Humberto Boncristiani wrote:
Hi.
I got cuffdiff files with gene differential expression on it. I don't
have the annotation, therefore I need to extract the sequence
information from the genome coordinates and them blast them to identify
those.
How the easiest way to do it?
Thanks.
Humberto
*Dr. Humberto Boncristiani*
National Research Council (NRC) Fellow
Adjunct Research Associate
Department of Biology
Univ. North Carolina at Greensboro
312 Eberhart Bldg
Greensboro, NC 27403, USA.
Tel.:(1) 336-256-2591
Fax: (1) 336-334-5839
email: [email protected] <mailto:[email protected]>
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___________________________________________________________
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:
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