Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • PacBio ENA SRA submission without bas.h5 files?

    Dear all,

    I've been sent some PacBio data from a collaborator that we now wish to submit to ENA. I've read that the way to do this is to create a manifest file, pointing to the 3 bax.h5 files, 1 bas.h5 file and 1 metadata.xml file for each cell (eg, this very useful post: http://seqanswers.com/forums/showthread.php?t=66767).

    However, for some reason (I don't know why) the bas.h5 files are not present: within each cell dir there are 3 bax.h5 files, 3 subreads.fastq files and 1 metadata.xml file. As I did not generate these data myself I don't know their exact provenance I'm afraid - I don't know if the sequencing centre at which they were generated simply failed to ship these files to my collaborator, of if they were mislaid later.

    The optimal solution would be to locate the missing files... but failing that, I wonder if anyone has had any experience of submitting to ENA without the bas.h5 files? Is it possible? Or, perhaps better, is there a tool/method that I can use to generate a bas.h5 file post hoc? My understanding of the bas.h5 files is that they are a "pointer" to the bax.h5 files, so maybe it's possible to make a new one.

    Any tips or potential workarounds would be much appreciated!
    Cheers!

  • #2
    Those files should have been generated from the primary analysis of the PacBio run. See details here.

    PacBio folks participate on the forum so perhaps they will have some advice later in the day.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X