ktan8
commented
1 year ago Hi Santiago,
That's a very interesting observation you have made here with Guppy 6.3 HAC. I have not tested this model out in our initial paper, and therefore have not observed this myself.
Given that these sequences are well-anchored to the subtelomere, my initial suspicion is that they are repeat calling errors as well.
One way to check if this is the case is to plot out the theoretical current profiles of (CCTGG)n repeats and (CCCTAA)n repeats, similar to what we have done in Supplementary Figure S15 of our Genome Biology paper. If you see that these sequences share similar current profiles, it would be a good indication that they were miscalled. Also, you would want to double check if these (CCTGG)n sequences are only observed on a single strand of the nanopore sequencing data. This would give you a sense of whether they are repeat artefacts as well.
Hope this helps.
KT
santiago-es
Hello,
I was wondering if new sequencing artefacts beyond what was described in the Genome Biology paper have been discovered now that Guppy has undergone several iterations since the version used in the publication.
For example, in many reads which are well-anchored to subtelomere, I often see degenerate telomere sequence that looks like this:
Often it will be immediately adjacent to canonical telomere repeats. In this case, this is the sequence I see on the C-rich strand.
This data was basecalled with the Guppy 6.3 HAC promethion basecaller (R9.4.1 chemistry, 400bps)
Would there be a way to test whether this is truly an artefactual telomere using your basecaller?