Pacbio CSS - coverage per locus

Question

[pingu77]

Hi All!

I have a question about Pacbio CSS data. Since the css step is supposed generate a final consensus sequence using the subreads, I am wondering if it possible to have more reads (consensus sequence) that map to the same locus. Shouldn't I have 1 reads for each locus? Or would it be possible to have a coverage higher than 1 in each locus? If so, why?

Thank you!

Answer 1

[William Rowell]

Hi pingu77,

It sounds like you're maybe confusing the output of CCS with the output of a de novo assembly tool like hifiasm.

I think there might be an XY problem here. It might be best if you contact [e-mail] and describe the high-level problem you're trying to address, for example "creating a de novo assembly from HiFi WGS data to view haplotypes" or "calling tandem repeat structural variants from targeted CLR data". If you're using a public dataset, in the email link the dataset. PacBio Support will be able to provide a high-level answer about whether/how the biological problem can be addressed with the data you have, and if it's possible, they can likely point you to the concrete steps you need to take to analyze the data.

Answer 2

[Istvan Albert]

The CCS reads mean that the fragment was long enough to be read multiple times. It refers to one DNA fragment being read multiple times (3 or more), those multiple reads are then consolidated into a single read of high accuracy.

It has no connection to how many reads cover a location.