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  • Error using Bowtie alignment mRNA seq

    Hi all,

    I am trying to map my mRNA-seq data using Bowtie (on Galaxy) with default parameter settings. The following error occurred. Does anyone know what this error means?

    Error aligning sequence. Error while flushing and closing output
    terminate called after throwing an instance of 'int'
    /bin/sh: line 1: 6367 Aborted bowtie -q -p 8 -S -n 1 -e 70 -l 28 -k 1 --phred33-quals /galaxy/data/calJac3/calJac3full/bowtie_index/calJac3full /galaxy/main_database/files/003/454/dataset_3454739.dat > /galaxy/main_pool/pool2/tmp/job_working_directory/3077957/galaxy_dataset_3457255.dat

    Maybe I am using illegal parameter settings, what parameters do people usually using to align mRNA-seq data?

    Thanks in advance for your help!

    -Eric

  • #2
    Eric,

    A quick search of the Galaxy mailing list archives (http://galaxy-users-list-archive.2308625.n4.nabble.com/) did not yield an answer for me.

    Try posting the question to the galaxy-user list. Subscribe at http://lists.bx.psu.edu/listinfo/galaxy-user.

    Comment


    • #3
      may be use TopHat instead?

      Comment

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