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  • Tophat - Error using Paired End

    I tried using Tophat for paired end analysis.

    [Tue Feb 9 23:26:32 2010] Mapping reads against m_musculus with Bowtie
    [Tue Feb 9 23:46:06 2010] Joining segment hits
    [Tue Feb 9 23:53:48 2010] Mapping reads against m_musculus with Bowtie
    [Tue Feb 10 00:13:47 2010] Joining segment hits
    [Tue Feb 10 00:20:47 2010] Searching for junctions via segment mapping
    Warning: junction database is empty!
    [Tue Feb 10 01:40:00 2010] Joining segment hits
    IOError: [Errno 28] No space left on drive

    Are these two separate errors? I'm going to try repartitioning so my harddrive has more space but I would have thought that ~30Gb would have been more than sufficient. Does paired-end analysis require that much more space? I've run non paired end samples successfully with Tophat on the same machine.

    If anyone can help, thanks!

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