gravatar for Smandape

2 hours ago by

United States

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 (such as this and this). 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 ([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' ( 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 the bam file doesn't say subreads in its filename. In such case what file is it?

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