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Hi @iiSeymour
We are using NVIDIA V100 GPU.
We have created an virtual environment to run bonito. For test training run, we have used a fast 5 file of size 152MB (corresponding to ~2750reads).
We…
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I am trying to model a protein homodimer complexed with dsDNA. I have entered in the two identical protein monomer chains as separate files and DNA strands as two separate files. In a command similar …
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Hello,
I am currently doing a basecalling model refinement and am running into some issues in the pre-processing basecalling step surrounding memory management.
Specifically, I have a folder of …
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I have an issue using the pre-prepared dataset from the command provided in the README.md
```
$ bonito download --training
$ bonito train --amp /data/training/model-dir
```
I have successfully …
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We've been applying Bonito to some of our PromethION datasets. However, we noticed that the model seems to be basecalling some repeat elements incorrectly. To address this, we figured that providing t…
ktan8 updated
3 years ago
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Dear,
I am leaving the Nanopore Day in Bordeaux and there Stephen Rudd presented the release of this promising tools.
What should be the size of the training set? Number of reads of the same ref…
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Hello,
I have a problem regarding using bonito to build my own methylation detection model on microalgae data. I do the following workflow :
```
$ git clone https://github.com/nanoporetech/bonito…
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We discussed this manuscript https://openreview.net/forum?id=S1gBgnR9Y7
Their setting is to use 1/3 of the images in the Cell Painting dataset that area also present in CHEMBL to predict 209 CHEMBL…
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Hi.
I found there is pretrained model for DNA model under
/models/mGru_flipflop_remapping_model_r9_DNA.checkpoint
but, is there any RNA model (model weight, or check point) for RNA?
Tha…
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Hello. I have followed all the required installation instructions and I'm testing it out. I have a pdb file and dcd trajectory inputted. It runs through the allotted time I give it on the cluster. How…