question about the parameters in Minknow configure file

novoalab / Nano-tRNAseq

Quantitative analysis of native tRNA populations using direct RNA nanopore sequencing (Lucas*, Pryszcz* et al., Nat Biotech 2023)

GNU General Public License v3.0

13 stars 5 forks source link

question about the parameters in Minknow configure file #2

Closed xieyy46 closed 1 year ago

xieyy46 commented 1 year ago

Hi developer! I am so confused about the parameters in the part analysis_configuration.read_classification in the Minknow configure file (as showed in below picture), would you please tell the details what median, local_median, median_before,local_range ect. mean ? And how dose this setting work to classify read？

lpryszcz commented 1 year ago

Hi @xieyy46 , to be honest we don't fully understand these parameters. We've been playing only with duration. I guess you could ask this directly to ONT ie via their community. Cheers,

xieyy46 commented 1 year ago

Hi lpryszcz, Thank you for your reply! By the way, do you know how adaptor signals were trimmed when using guppy basecalling for dRNA sequencing?

enovoa commented 1 year ago

Hi @xieyy46, for details on how guppy or other ONT-specific software works, please ask directly to ONT via their community, as @lpryszcz already mentioned in this previous response. Thanks!