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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