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Various questions about Remora

8

Hello, I have a few questions that are not really related to each other. First: I always assumed when training and running the model on new data, you had to...

tcb72

Insect 5hmC values anomalous

3

I am working with an insect genome and trying to call 5mC and optionally 5hmC. When using megalodon with `--remora-modified-bases dna_r9.4.1_e8` model calling 5mC only, I get around 6% 5mC...

dithiii

R10.4 250bps signal to base mapping

1

I am trying to prepare a dataset for base modification detection that has been sequenced on a MinION device using an R10.4 flow cell at high accuracy mode 250bps. Checking...

marcpaga

Correct model to use for 5hmC calling

1

Not sure if this should be a bonito issue or a remora issue. I run the following: ``` bonito basecaller [email protected] $input_path --modified-bases 5mC 5hmC --reference $reference > basecalls_with_mods.sam ```...

rlowe-altoslabs

how to interpret the results from "remora infer from_taiyaki_mapped_signal"

8

Thanks for the great tool! Just wondering how the "read_pos" in the results from "remora infer from_taiyaki_mapped_signal" are chosen - so which positions of a read are shown in the...

jon-xu

Multiple GPU device

2

Hi @marcus1487 , I was wondering is it possible to specify multiple GPU devices for Remora during training? like --device 0 1 2 Thanks, Vahid

vahidAK

Model improvement questions

4

Greetings, This is mostly about how to improve the quality of remora models and a few other questions will be asked below. I have trained a custom modification remora model...

jorisbalc

Data preparation scripts for Remora models with random bases

2

Hello Remora Team, In this year's ONT update, Clive mentioned that the newer models that perform better than BS-seq are trained with sequences that contain a modified position with +-30...

AnWiercze

Question about data preparation for training model

1

Hi, I understand that to train a model using remora you first have to basecall fully unmethylated (pcr) or fully methylated reads (sssI) then merge both result to build a...

pterzian

Remora re-squiggle (refine_signal_map.SigMapRefiner) on RNA data

4

Dear ONT team, I am trying to re-squiggle my RNA data using Remora after I basecalled the data with Dorado. Comparing the analysis from Tombo and Remora on the same...

mem3nto0