hd2326

@iiSeymour Thank you very much for the quick reply! So the mod-calling will be a two-step process, 1) using bonito tar+toml for basealling, based on which 2) using remora onnx...

Got it! Thank you so much for the explanation!

Greetings! As I am running bonito as @iiSeymour suggested: bonito basecaller $bonito_models/[email protected]/ $rawdata --modified-base-model $remora_model/model_best.onnx --modified-bases $mod --reference $genome I got the following error: remora.RemoraError: No trained Remora models for...

Awesome! As @marcus1487 suggested, removing `--modified-bases` solves the problem! But another problem came... It seems that the bonito bam files are not compatible with `samtools mpileup` for modification analysis. I...

@najohink Actually no. Still the same error...

Same exact error here. And there is another thing that confuses me. Since @89213385 mentioned about #reads, I checked the output of "bonito basecaller --save-ctc". The training set contains ~800...

Hey @vjcitn thank you very much for your help and suggestions! I re-formatted the vignette as an Rmd, and provided more explanations on the package. I also confirm that the...

Greetings @vjcitn ! Just want to know if there is any update on the review process. Thank you very much!

Hey @vjcitn sorry for the delay. As per your request, we added an "introduction" section to provide the scientific background and motivation. We also revised the headings to remove abbreviations....