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bowtie - windows instalation



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  • bowtie - windows instalation

    I am trying Bowtie. It seams very fast and efficient!
    However I have a minor problem in my installation (windows XP)

    1 - I downloaded Bowtie from the link
    file: bowtie-

    2 - Unzipped to C:/bowtie

    3 - Test it:

    bowtie -t e_coli reads/e_coli_1000.fq e_coli.map

    Bowtie website says:
    "This run calculates the same alignments as the previous run, but the alignments are written to e_coli.map (the final argument) rather than to the screen. Also, the -t option instructs Bowtie to print timing statistics, which will look something like this (times will obviously differ):

    Time loading forward index: 00:00:00
    Time loading mirror index: 00:00:00
    Seeded quality full-index search: 00:00:01
    Reported 699 alignments to 1 output stream(s)
    Time searching: 00:00:01
    Overall time: 00:00:01


    However in my computer the output stops after the first two lines and stays like that forever if I let him.
    Something like this:

    Time loading forward index: 00:00:00
    Time loading mirror index: 00:00:00

    When I check the file with the results (e_coli.map) it seams complete. With the 699 lines...

    I am not sure if I should have done some compilation or installation of Bowtie before starting the runs. I merely downloaded it into a folder and execute the command..
    Any ideas or thoughts?


  • #2
    Hi Ines,

    I am aware of this problem and am going to take a look at it soon. It most likely has something to do with the MinGW pthreads library.

    No, you don't need to do any compilation or installation beyond just unzipping the package - the error is my fault.



    • #3
      bowtie runs well in cygwin.
      would a windows installation be preferable over a linux one in cygwin?


      • #4
        dear All,

        I have recently joint the forum, it is interesting. Actually i want to use Bowite Tool for 72 bp fragments of illumina read (microbail genome) assembling via windowXp based operating system. could any one guide me from very basics of window based installation and operation of this tool. Previously i have assemble a genome with DNAStar tool. Any body could help please. ? his/her help will be highly appreciated.

        Asifullah Khan


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