Closed billytcl closed 3 months ago
Hi @billytcl - can you try to run the dorado basecaller
command with then --no-trim
option? I suspect that adapter trimming may be getting in the way of barcode classification, so running with no-trim will help validate that theory
Sure thing! Will give it a shot. If it does interfere with barcoding shouldn’t it then be off by default when barcoding is on?
On Mon, Mar 4, 2024 at 6:58 PM Joyjit Daw @.***> wrote:
Hi @billytcl https://github.com/billytcl - can you try to run the dorado basecaller command with then --no-trim option? I suspect that adapter trimming may be getting in the way of barcode classification, so running with no-trim will help validate that theory
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Hi @billytcl - I want to confirm that's indeed the case for your situation. We have some improvements along that line internally for the next release already, and your input would help determine if more changes are needed.
Ok! This may take a few days for the run to finish basecalling.
@billytcl did you get a chance to give this a go? I am interested in your result too!
Closing due to inactivity. FYI @billytcl we have improved the interplay between adapter trimming and barcoding within dorado since 0.6.0 release, so this should be less of a problem now
Issue Report
Please describe the issue:
I am using the Native Barcoding 96 kit with R10.4.1 5kHz, and I'm observing a huge difference between ont-dorado-server and dorado standalone. It's ~10-20% difference with more reads classified with ont-dorado-server and more being unclassified with dorado standalone. I am using a different methylation model but I highly doubt that's the culprit. I'm thinking there may be a weird interaction with read splitting that's different with standalone dorado?
ont-dorado-server v7.0.8
dorado 0.5.3
Run environment: