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  • Coryza
    Member
    • Feb 2014
    • 29
    #1

    Bowtie2 - Own Indexes

    I was wondering... perhaps it's a really stupid question but ok. I've got +- 100 control sequences, is it possible to build an own '6 indexes (bt2)' out of that via the bowtie2-build. So that I'm able to map all my RNAseq sequences against these controls?

    And if so, what parameters should I use? Because I know used -hg19 for the genome indexes.
    Tags: None
    • GenoMax
      Senior Member
      • Feb 2008
      • 7142
      #2
      http://bowtie-bio.sourceforge.net/bo...-build-indexer

      Keep the order of command line options as indicated on the help page.

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