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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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[improvement] dorado trim says 'basecalled' instead of amount of bases trimmed #988

Open JWDebler opened 1 month ago

JWDebler commented 1 month ago

Hi, I was just processing a bunch of reads with dorado trim (0.7.3) and noticed that it keeps saying:

[info] > Simplex reads basecalled: 456331

And if I turn verbose on:

[debug] Total reads processed: 456331
[info] > Simplex reads basecalled: 456331

That doesn't really make sense for the trimming module. I'd be much more interested if it could tell me something like:

x bp barcodeXX trimmed
x bp adapter trimmed

Cheers, Johannes

HalfPhoton commented 1 month ago

Thanks for bringing this to our attention - we'll update this.

JWDebler commented 3 weeks ago

It is also still leaving lots of barcodes on the reads.... at this point i'm probably just going to hard trim 100 bp off each end instead of relying on dorado trim.

JWDebler commented 3 weeks ago

I just had another read of the main page, am I understanding it correctly that dorado trim only trims adapters and primers if I feed i an already demultiplexed fastq file, and it isn't checking for barcodes? If so, can this please added?