Closed gambalab closed 1 month ago
Hi @gambalab,
Q1. Yes - the FASTQ output will have all 3 "read types". I'm not sure if there's any way to find which reads are which other than;
Q2 - The adapters that are not trimmed in simplex basecalling are rapid adapters.
Best regards, Rich
thank for your prompt answer. So, regarding Q2, is it correct to use dorado trim
command?
Or wold be more correct use dorado trim --no-trim-primers
that should trim only adapters in this way?
I believe the standard basecall settings should be sufficient and no additional trimming is needed.
Dear Dorado Team,
Thank you for developing the valuable Dorado tool.
I have a question regarding generating FASTQ files using the
--emit-fastq
parameter with thedorado duplex
command. I understand that FASTQ format doesn't include thedx
tag, which identifies reads originating from duplex or simplex calls. However, I have specific concerns:Read Types in FASTQ Output: Does the FASTQ file generated by dorado duplex contain all three read types: (i) Duplex reads (ii) Simplex reads without duplex offspring (iii) Simplex reads with duplex offspring? Or it only contain just the first two types (duplex and simplex without duplex offspring)? his last behavior would be ideal since simplex reads that had a duplex offspring are just a duplicated read with more errors and could negatively affect variant calling accuracy.
Adapter Trimming for Simplex Reads: Since dorado duplex reportedly doesn't trim adapters in simplex reads, would it be appropriate to run
dorado trim
on the resulting FASTQ files for adapter removal before alignment?Thank you for your clarification. I look forward to your response.