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Old 11-29-2020, 04:36 PM   #1
smandape1
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Default 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?
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Old 11-29-2020, 05:47 PM   #2
GenoMax
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Cross-posted for reference: https://www.biostars.org/p/476158/
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genome, pacbio, pacbio ccs readsofinsert, sequencing, sra

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