input signal data of deepsignal

[sengelen]

Hi Peng

I have many nanopore sequencing runs from an arabidopsis strain with fail and pass data. I was wondering if it is better take all the data, only pass data or only data from the same sequencing run ? And which coverage do you recommend ?

Best
Stefan

[PengNi]

Hi Stefan, for arabidopsis I'd recommend 40-100x coverage of reads. I recommend to use PASS reads only if you have enough PASS data. I am not sure if there is any significant batch effect if you use data from different runs.

Best,
Peng

[sengelen]

Thank you

Best,
Stefan