Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Ploidy estimation or decision using pacbio sequel data yjpark1091 Bioinformatics 1 04-29-2018 11:46 AM
Genome assembly using Pacbio sequel data yjpark1091 Pacific Biosciences 5 11-29-2017 09:32 AM
variant calling from pacBio Sequel data splaisan Bioinformatics 0 03-25-2017 07:20 AM
Uploading PacBio raw data to ENA SRA maubp Pacific Biosciences 13 03-11-2016 07:07 AM
PacBio data - problem with SRA toolkit Retro Pacific Biosciences 7 12-04-2015 06:56 AM

Thread Tools
Old 11-29-2020, 04:36 PM   #1
Junior Member
Location: Indianapolis

Join Date: Oct 2011
Posts: 2
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 ([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?
smandape1 is offline   Reply With Quote
Old 11-29-2020, 05:47 PM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,087

Cross-posted for reference:
GenoMax is offline   Reply With Quote

genome, pacbio, pacbio ccs readsofinsert, sequencing, sra

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:15 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO