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remora 3.0: error when training on different canonical bases

9

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...

Mathias-Boulanger

Urgent Help: Cannot Speed up Metric Extraction script

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Hello, I have been working on trying to extract metrics with remora on a very large nanopore dataset. I am running into issues with the speed at which I can...

alexturcoo

100% training accuracy - unable to navigate mistake

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Hi Marcus, I managed to make a dataset that has separate 10+ nucleotide handles on either side of the unmod G and mod G randomers with the structure: `LeftHandle1-NNNNGNNNN-RightHandle1` and...

moa4020

Add RNA Models to Pretrained Folder

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Hello, We are trying to use Remora based off of a pretrained model, but are working with RNA. Would it be possible to add the RNA models that are currently...

VBHerrenC

```get_io_reads()``` fails with ```Move table discordant with signal``` on some reads

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Hi @marcus1487, I am running into an issue that I was hoping you could provide some insight into: I have a dataset from a P2 sequencer that was basecalled and...

drivenbyentropy

Alternative model

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Hello, I would like to ask if, in the absence of a reference sample without modifications, I can still use the program for methylation detection. Is there perhaps some alternative...

philipmories

the exact meaning of different fields in remora dataset prepare output

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Hi remora team, Cheer for your good work! I want know what the data of different fields (shown in below figure) in remora dataset prepare output exactly mean? 

xieyy46

What causes differences in meth_qual distributions between samples?

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Looking at a few cfDNA samples across different runs, we've noticed instances where the meth_qual distribution can vary widely quite a bit. Eg. some samples are strongly piled up near...

billytcl

Add query to ref coord mapping

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targeting spliced read issue https://github.com/nanoporetech/remora/issues/118#issue-1925040269

chilampoon

ref to signal mapping did not consider splicing

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Hi @marcus1487, I was using remora API on real direct RNA-seq data, but ran into errors from this command: ```python io_read = Read.from_pod5_and_alignment( pod5_read_record=pod5_reads[bam_read.query_name], alignment_record=bam_read, reverse_signal=True, ) ``` ``` ---------------------------------------------------------------------------...

chilampoon