Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      The Impact of AI in Genomic Medicine
      by seqadmin



      Article Coming Soon......
      Today, 02:07 PM
    • seqadmin
      Multiomics Techniques Advancing Disease Research
      by seqadmin


      New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

      A major leap in the field has
      ...
      02-08-2024, 06:33 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 02-23-2024, 04:11 PM
    0 responses
    32 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-21-2024, 08:52 AM
    0 responses
    46 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-20-2024, 08:57 AM
    0 responses
    37 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-14-2024, 09:19 AM
    0 responses
    63 views
    0 likes
    Last Post seqadmin  
    Working...
    X