Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Analyzing PacBio sequel data and SRA

    I am new to NCBI's SRA and pacbio sequencing data analysis. I am trying to download pacbio sequence data from SRA and my goal is get CCS (Consensus) reads [fastq/a format is best]. The data is generated from PacBio's sequel instrument. What I read so far relates to the data analysis methods from their previous instrument (RS II). I referred to online blogs and Biostars posts. My questions are related to both SRA and pacbio sequence data:

    1. What do runs mean in SRA (for example HG00733) when filtered for (Source: DNA, Platform: PacBioSMRT) on right yields 7 experiments. Some of them have multiple runs for an experiment. For example, this is a WGS on Sequel II and has 7 runs. The only difference I found between these runs is different library name but for other experiments with multiple runs I didn't find anything different between runs.

    2. I am particularly interested in this experiment (https://www.ncbi.nlm.nih.gov/sra/SRX4480530[accn]). I want to get consensus reads for this experiment. What I read from other posts say it is easy to start with raw data or subreads files. I went to the 'Data access' page for this experiment's run but there are multiple subreads.bam files in the 'Original format' (https://trace.ncbi.nlm.nih.gov/Trace...run=SRR7615963). My question is what does it mean when there are multiple subreads.bam files? And how do I get consensus reads from multiple bam files? I read about SMRTlink binary software and Canu to process subreads.bam to get consensus. Which tool should I use here? Or is there a direct way to get consensus reads from SRA?

    3. For the experiment mentioned above (SRX4480530), the original format bam files say subreads.bam but for other experiments (such as https://trace.ncbi.nlm.nih.gov/Trace...run=ERR3822935) the bam file doesn't say subreads in its filename. In such case what file is it?

  • #2
    Cross-posted for reference: https://www.biostars.org/p/476158/

    Comment

    Latest Articles

    Collapse

    • seqadmin
      The Impact of AI in Genomic Medicine
      by seqadmin



      Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
      02-26-2024, 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, 02-28-2024, 06:12 AM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-23-2024, 04:11 PM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-21-2024, 08:52 AM
    0 responses
    77 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-20-2024, 08:57 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X