Header Leaderboard Ad


PacBio ENA SRA submission without bas.h5 files?



No announcement yet.
  • 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!

  • #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.


    Latest Articles


    • seqadmin
      A Brief Overview and Common Challenges in Single-cell Sequencing Analysis
      by seqadmin

      ​​​​​​The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i...

      01-24-2023, 01:19 PM
    • seqadmin
      Introduction to Single-Cell Sequencing
      by seqadmin
      Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.

      The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes
      01-09-2023, 03:10 PM