3 ms·
Are you sure about that? My last consensus run worked with complete coverage of ~410 bp region. Here is a gist of the raw pileup without consensus - https://gis
by koeng 6y ago
Are you sure about that? My last consensus run worked with complete coverage of ~410 bp region. Here is a gist of the raw pileup without consensus - https://gist.github.com/Koeng101/abc674e1acd575646748afcbcc74698d https://gist.github.com/Koeng101/abc674e1acd575646748afcbcc7...
Visually, I think, you can see that it isn't THAT bad (low coverage at the ends is because of how I barcoded the sequences).
I hate to be that guy, but have you actually used the technology? And if so, approximately what year? Unacceptable for what procedure? Do you have any raw reads that have been troubling you?
- searine 6y agoThey mean at genome-wide scales. If you are just doing a 410bp the sequence is short enough that the signal of is going crush and noise you get from strands slipping in the pores. The errors nanopores get are gaps, not base pair substitutions. So with things like viral or bacterial sequencing you don't really have huge issues. When you are doing large eukaryotic sequences with lower coverage on average, you start picking up a lot of deletion artifacts. Which isn't a huge deal if you have a very well annotated genome like human, but if you are doing pioneer genomics it can create some difficulties. Often if the genome isn't well annotated, its best to pair nanopore with short reads.
- koeng 6y agoThe gaps are usually homopolymers and such, which should get helped by R10 pores. But true, at low coverage, things can get tougher!