Hi Kanwar,
To use a custom genome, all you need to load is the .fasta file of the
genome. Galaxy will do the indexing as part of the mapping job when it
is launched.
Help with custom genomes in is this wiki:
http://wiki.galaxyproject.org/Support#Custom_reference_genome
Hopefully this helps to simplify things!
Jen
Galaxy team
On 11/26/12 2:56 AM, shamsher jagat wrote:
I have a Hi-seq Single end data and want to align it to a viral genome
and have fasta file of viral genome. I have created index files out
side Galaxy (I believe I cannot create index file with in Galaxy). The
question which I have is:
There are various index files (v.fasta.amb; v.fasta.pac; v.fasta.rbwt;
v.fasta.rpac; v.fasta.sa <http://v.fasta.sa>) should I be using all
the these files as zip file for index file or one (which one?).
Thanks
Kanwar
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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:
http://lists.bx.psu.edu/
