Post #979297
2026-04-07 13:04 UTC
Dear Nanopore folks, could you give an advice about an issue that my lab has with direct RNA sequencing on MinION. We're doing RNA004 sequencing of various samples and again and again, there's a staggering amount of reads with just repetitive AAG triplet. This happens for weird IVT RNA and perfectly normal yeast or HEK cells. I'm using Dorado 1.4.0 with the 5.3.0 sup model. Looks to me like the open channel or some kind of stalling is just called as this kmer.
#nanopore #nanoporesequencing
Replies (2)
-
@mzdravkov@mastodon.green 2026-04-07 13:18
PS. the issue appears across completely different samples, different batches of flow cells, different people preparing and loading the samples, two different MinION devices (Mk1B and Mk1D).
-
@lpryszcz@genomic.social 2026-04-07 13:30
@mzdravkov@mastodon.green we've observed that in all runs, usually a few % of reads, sometimes over 10%. When you plot raw signals, you'll see strange stretches similar to homopolymer... we haven't observe anything like this in rna002, only in rna004. my working hypothesis it that's because of helicase #stalling specific to new #RNA #helicase variant used in #rna004 @nanopore@genomic.social