Comments (2)
First off, I wouldn't use NGMLR these days.
You can input unaligned SAM into minimap2 using:
samtools fastq -T "*" <input> | minimap2 ... | samtools view ....
This will preserve all tags in the output from dorado. (Note that -T "*"
needs to latest samtools). See this nextflow snippet for a more complete example.
I would not try piping directly from dorado to minimap2 at this point --- I and @SamStudio8 experienced oddities doing this.
from dorado.
Thanks for the hint!
from dorado.
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from dorado.