One question about dorado basecalling trim option

[dolittle007]

Hi team,

Since Pychopper uses primers (SSP, VNP) for classifying the reads, the primers should be kept during dorado basecalling.

While dorado --trim option takes as its argument one of the following values:

• all: This is the the same as the default behavior. Any detected adapters or primers will be trimmed, and if barcoding is enabled then any detected barcodes will be trimmed.
• primers: This will result in any detected adapters or primers being trimmed, but if barcoding is enabled the barcode sequences will not be trimmed.
• adapters: This will result in any detected adapters being trimmed, but primers will not be trimmed, and if barcoding is enabled then barcodes will not be trimmed either.
• none: This is the same as using the --no-trim option. Nothing will be trimmed.

According to the above description, --trim adapters should be used, am I right?

Thanks a lot in advance.

[nrhorner]

Hi @dolittle007

I think you should be able to use --trim adapters or --no-trim and still have your primer sequences in your reads.

Thanks

[dolittle007]

Hi @nrhorner, I have tried --trim adapters. It works well. Thanks a lot.