-
Hi! I'm new to this and I have no idea what is wrong. GeneMarkES/ST is an application in my university's HPC system, so I did not download the GeneMarkES program on my own computer (my genome files ar…
-
Hi, thanks for your amazing work
I wanted to ask about sharing the training code and data?
for RNA/DNA data all of the thing I see in repo are sequences. could you please share pdb files
Than…
-
Hi there,
I am trying to simulate nanopore amplicon reads (~6.5 kbp longest amplicon, ~37 kb total sequence) but the simulation part seems to hang and never proceed. I was able to train an error pr…
-
https://github.com/bcgsc/NanoSim/issues/11#issue-204760214 This bug happened again:
(nanosim_env) lishuxian@tong1:/mnt/md0/LSX/lishuxian/lishuxian/mag/LSX-isolates/Kleb-for-lsx/bin-file$ cat list.fas…
-
Hi,
I am trying to run reptile on pre-trained model mm_model_coreMarks.reptile using methylation data. Is there any issue with bw generation, I have methylation base call bed files containing chr no,…
-
```shell
atrix@Atrix:/mnt/c/Users/adity/OneDrive/Desktop/dnabert/DNABERT_2-main/finetune/Scripts$ sh run_dnabert2_new.sh /mnt/c/Users/adity/OneDrive/Desktop/dnabert/GUE
The provided data_path is /mn…
-
Hi,
I have noticed a lot of errors in the taxonomy ranks when looking at the names. At first, I used the already trained version (4.13) when I noticed the problem. I decided to use the pr2_version_…
-
Hello!
I would like to build the custom model using bonito because some repeat sequences have basecalling errors in the default DNA model. And I have two questions.
1. I noticed that in bonito t…
-
https://doi.org/10.5220/0006636401400145
> In the era of precision medicine and cancer genomics, data are being generated so quickly that it is difficult to fully appreciate the extent of what is d…
-
Hi @iiSeymour
We are using Tesla V100. We have used the "bonito download --training" to download bonito training dataset. It showed around 12Gb.
Now, it is more than 17 hrs since we started the do…