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  • index reference file to use for bowtie

    I am trying to run Bowtie on a small test fastq file. It is human hg19 build. I found that the index file can be downloaded from the right panel of this:



    The downloaded files are:

    hg19.1.bt2
    hg19.2.bt2
    hg19.3.bt2
    hg19.4.bt2
    hg19.rev.1.bt2
    hg19.rev.2.bt2
    hg19.zip
    make_hg19.sh

    make_hg19.sh requires bowtie2. and I don't have authorization to install bowtie2 onto our server.

    Since hg19 must be a very common reference, is there anyplace that we can directly download the indexed file of hg19? what is the appendix for this index file?

    thanks

  • #2
    Bowtie(1) needs a Bowtie(1) library, it can't use a Bowtie2 library. Assuming you already have Bowtie installed then make the library using the 'bowtie-build' command. You should upgrade to bowtie2 though, it is much better.

    Comment


    • #3
      Thanks I see

      Comment

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