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) should I be using all the these files as zip file for index file or one (which one?). Thanks Kanwar
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