Question: Pacbio Ccs Vs Subreads Explained ?
gravatar for curious.genome
6.3 years ago by
curious.genome40 wrote:

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

Thanks for your help!

ADD COMMENTlink modified 5.8 years ago by Biostar ♦♦ 20 • written 6.3 years ago by curious.genome40

You asked the same question at seqanswers, where it was answered nicely. See

ADD REPLYlink written 6.3 years ago by lexnederbragt1.2k

Question was helpful. Thank you.

ADD REPLYlink written 5.8 years ago by Prakki Rama2.4k
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