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  • Missing accepted_hits.bam and junctions.bed files

    I am a new user of TopHat and I am still feeling my way around it. I ran TopHat to align some RNA seq data to known gene models. The program apparently ran successfully, as no error messages were thrown. However, I could find no accepted_hits.bam file or junctions.bed files as output.

    Some earlier threads mentioned this problem, but as far as I could tell no solution was ever presented.

    I would appreciate any insight into this problem. Thank you.

  • #2
    We had the same problem when we had 1 machine with 20Gb running tophat and it would stop with no message apparently when it reached about 70% of the disk space (the output of tophat is very large!).
    We added another disk with 20Gb and run again, pointing the output to the new disk and it worked fine.
    The last line in tophat.log file should be something like:
    Run complete: 04:34:35 elapsed
    When we were running out of disk, the last line was:
    Searching for junctions via segment mapping
    And nothing else, no error message.
    I hope that helps.

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