When doing dorado basecall an option exists to look for primers that are not from ONT kits --primer-sequences but this doesn't exist for dorado trim . I've checked and it is not identifying other primers by default but it is successfully removing the ONT adaptors. However, when checking the output in verbose mode in each step it says 0 reads are being processed which if referring to reads with trimmed adapters, is clearly false.
These functionalities are important because when duplex basecalling, adapters and primers can not be trimmed.
Thanks
When doing dorado basecall an option exists to look for primers that are not from ONT kits
--primer-sequencesbut this doesn't exist fordorado trim. I've checked and it is not identifying other primers by default but it is successfully removing the ONT adaptors. However, when checking the output in verbose mode in each step it says0 reads are being processedwhich if referring to reads with trimmed adapters, is clearly false.These functionalities are important because when duplex basecalling, adapters and primers can not be trimmed. Thanks