Question: Pacbio Ccs Vs Subreads Explained ?
4
gravatar for curious.genome
5.4 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!

• 9.7k views
ADD COMMENTlink modified 4.9 years ago by Biostar ♦♦ 20 • written 5.4 years ago by curious.genome40
2

You asked the same question at seqanswers, where it was answered nicely. See http://seqanswers.com/forums/showthread.php?t=34790

ADD REPLYlink written 5.4 years ago by lexnederbragt1.2k

Question was helpful. Thank you.

ADD REPLYlink written 4.9 years ago by Prakki Rama2.2k
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