Hi guys,
I've been trying to understand PacBio data for a while now, I think that it's the way forward for our lab. I'm still having trouble understanding CCS though - my biology is quite shaky.
1. Could someone explain to a computer scientist - how does PacBio get its CCS from the subreads or long reads ?
2. Our collaborators with the PacBio data gave us a set of files - with subreads.fastq, CCS.fastq and long_reads.fastq. When I ran a FASTQC report for subreads, I got base quality scores of around 10-15, whereas with CCS I got a larger variation for quality scores with values between 30-40. Is this expected ?
3. Which of these files should I use to perform assembly ? I'm guessing it's CCS.fastq
Sincerely,
Confused-in-pacbio-land
I've been trying to understand PacBio data for a while now, I think that it's the way forward for our lab. I'm still having trouble understanding CCS though - my biology is quite shaky.
1. Could someone explain to a computer scientist - how does PacBio get its CCS from the subreads or long reads ?
2. Our collaborators with the PacBio data gave us a set of files - with subreads.fastq, CCS.fastq and long_reads.fastq. When I ran a FASTQC report for subreads, I got base quality scores of around 10-15, whereas with CCS I got a larger variation for quality scores with values between 30-40. Is this expected ?
3. Which of these files should I use to perform assembly ? I'm guessing it's CCS.fastq
Sincerely,
Confused-in-pacbio-land
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