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hasindu2008 / squigulator

a tool for simulating nanopore raw signal data
https://hasindu2008.github.io/squigulator
MIT License
58 stars 3 forks source link

4kHz vs 5kHz #15

Open awgymer opened 4 months ago

awgymer commented 4 months ago

Can this tool account for differences between the 4kHz and 5kHz sampling frequency (switchover after ONT sequencing software version 23.04)?

hasindu2008 commented 4 months ago

Yes. The latest squigulator v0.3.0 with the -x dna-r10-min and -x dna-r10-prom profiles generate 5KHz data by default. If you want old 4KHz data, specify -f 4000 along with -x dna-r10-min or -x dna-r10-prom. Hope it is clear enough?

awgymer commented 4 months ago

Ideal, thank you!

awgymer commented 4 months ago

Sorry I am now looking at running this and I realise I'm not sure I fully understand the logic behind -f 4000?

This simply sets the coverage depth to 4000 I thought? I'm not sure how this would relate to the data sampling frequency of 4 vs 5 kHz.

Perhaps I have to just use two versions of squigulator to get r10 data at both 4k and 5k sample rate?

hasindu2008 commented 4 months ago

Oh my bad. I told you the wrong option. You should be using --sample-rate not -f. Sorry about the inconvenience.

awgymer commented 4 months ago

No worries, thanks for the clarification