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SMRT View - How to examine resequencing data

When generating secondary analysis data from PacBio sequencing, you can use the SMRT View with your data, but the visual representation does not seem intuitive/friendly to me.

  1. How does one look at the variants table in a resequencing job?
  2. How can you determine an obvious, big indel when variants doesn't reflect an obvious say 1Kb deletion?
  3. What type of quality measure is the QV (apart from it being "four different per-base Quality Values")? Better yet, what's a good quality cutoff?
  4. Any other visualization programs out there that will display PacBio analysis data?

Off-topic question...

  1. What's a typical good coverage cutoff, 30x or 50x?
pacbio sequencing smrtanalysis smrtview
• 1,776 views • link
written by me • me

Have you looked at the manual? Not many on here are going to have access to SMRT view.

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written by GenoMax GenoMax

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