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# Issue Report
## Please describe the issue:
Hi, if I give Dorado an amplicon repeat set of pod5's (in this case CGG) would read splitting affect the generation of FASTQs for this? I have a PCR …
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Hello,
I'm trying to fine tune a model with large repeat expansions (>500 hexamer repeats), where the standard model hallucinates biologically impossible repeats. The issue is that the number of re…
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# Issue Report
I am trying to understand how the mean quality scores in the `qs` tag are calculated. Here is one entry from my base called .bam file (loaded into R).
```
> dat
[1] "01d312cc-5…
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When using dorado for duplex basecalling without providing a pair id file the duplex rate is below 1% when provided with a pair id file created with duplex tools the duplex rate is above 30%. I am usi…
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Am I understanding it correctly that when you call CpGs using modekit pileup with the -ref flag, only the CpGs that are present in the reference genome will get called? And any site that is a CpG in y…
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Hi,
I got an error (c.f below) when running `remora dataset prepare` using multiple focus bases. I already trained models in the same spirit using remora 2.0, that why I don't know if that's an e…
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## Issue Description
Using summary table from Dorado to subset POD5 leads to error for split reads which are assigned new IDs during demux. Also encountering a sys error but able to run without any *…
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Dear developers, thank you for quick improving of dorado!
But I think there is never too much documentation. For example, I still don’t understand in which subcommand the read splitting (by mid str…
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[dorado_error.txt](https://github.com/nanoporetech/dorado/files/13191818/dorado_error.txt)
Looks as though there's a bug with PyTorch that crashes the last steps..Error 1 and Error 2 when compiling…
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### Prerequisites
- [X] I have written a descriptive issue title.
- [X] I have searched all issues/PRs to ensure it has not already been reported or fixed.
- [X] I have verified that I am using the l…