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  • Drinkwater Lab

  • mPrime home

  • Using a bowtie server

    Running the bowtie alignments on a server will allow you to avoid downloading the large (approx. 3 Gb) genome index files as well as yielding faster performance.

    Setting up your own bowtie server is fairly straightforward if you have access to a php-enabled web server (ideally, apache running on a 64-bit version of Linux, with at least 8 Gb of memory).

    1. Download the bowtie server scripts (bowtie-server.tar.gz) and extract the archive. You will have a new folder labeled "bowtie".
    2. Move this folder to a convenient place within your web site (e.g., /var/www/html/mypages/bowtie).
    3. Copy the appropriate bowtie executable to the bowtie folder. For a 64-bit version of Linux, download and install the 64-bit Linux version of mPrime and copy the bowtie executable from the "bin" subdirectory of mPrime.
    4. Download the whole genome indexes for all three species (see the "Download indexes" link at left). Extract the files and copy all of the *.ebwt files to the "indexes" folder in your bowtie server installation.
    5. Assuming that /var/www/html is the root directory for your web site, located at "http://www.mysite.edu", and your bowtie directory is located at /var/www/html/mypages/bowtie, you would enter "http://www.mysite.edu/mypages" in the Bowtie URL box of the mPrime preferences dialog. Note the absence of "/bowtie" in that URL.

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