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  • ERANGE problems!

    Hi,

    I'm new to RNA-seq and am trying to use ERAGNE to map reads to the mouse genome using Bowtie v0.10.0. I've got my alignment and have created and indexed my .rds file from this. When I run the runStandardAnalysis.sh script it finishes in ~5 minutes with no RPKM values... very little appears to happen at the geneMrnaCounts.py, which completes almost instantly :-

    -------------------------------------------------------------------------
    runStandardAnalysis.sh mouse BTG1 ../RepeatMask/mm9.fa.out
    runStandardAnalysis.sh: version 3.6
    running with settings: mouse BTG1 ../RepeatMask/mm9.fa.out
    psyco not running
    /software/caltech/ERANGE/geneMrnaCounts.py: version 4.7
    marking NM
    caching ....
    dataset BTG1.rds
    metadata:
    bowtie_mapped True
    dataType RNA
    paired True
    rdsVersion 1.1
    readsize 51

    4983482 unique reads, 1003996 spliced reads and 674478 multireads
    default cache size is 10000000 pages
    found index
    getting gene features....
    getting geneIDs....

    -------------------------------------------------------------------------

    As you can see, no gene features or IDs are imported at this point, should they be? Does anybody have any idea what may be causing my problems?

    Cheers,
    Graham
    Last edited by gthomas; 01-11-2010, 04:35 AM.

  • #2
    ##########
    Last edited by gthomas; 01-12-2010, 04:40 AM.

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