Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how to get the fastq file from bax.h5 pacbio

    Hello guys

    Recently I have received my PacBio files from the company, which contain the sequencing results. The files are compressed (tar.bz2), when i extracted the file, I found only one file (name_of_the_file.bax.h5), I was wondering what would be the best way to analyse the file, as I am interested in the fastq file. How could i extract the fastq file?

    Many thanks

  • #2
    What kind of analysis are you running on the data, you often need to run through some PacBio specific software before getting data that can be analysed using standard tools. Minimally PacBio's filtering pipeline should be used to generate fastq.
    PacBio h5 format
    Simple tool for manipulating PacBio h5 files

    Comment


    • #3
      Thanks rhall

      I am interested in the consensus subreads, fastq. I want to align against known reference for SNP detection

      Many thanks

      Comment


      • #4
        If you don't want to install the full SMRT Analysis system, I would at least use pbalign to align the data, which can use the bax.h5 files, then use quiver to call SNPs, you will get much better results than using other aligners of consensus callers.

        Comment


        • #5
          Thanks very much Rhall, I will try this. Much appreciated.

          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
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          51 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          68 views
          0 likes
          Last Post seqadmin  
          Working...
          X