kir1to455

Calling cpggpc methylation with nanopolish

3

Hi, When I used nanopolish to repeat the nanoNOMe experiment, I found that my correlation was lower than nanoNOMe to compare with WGBS. Here is my nanopolish code: /nanopolish-cpggpc_new_train/nanopolish call-methylation...

Hi, marcus I'm trying to analyze m6A modification for a set of direct RNA data from ONT. I want to know if the version of guppy(v3.6.1 or v4 or v5...

Do CHEUI models work on SARS-CoV-2 RNA modification detection?

1

Hi, Thank you for developing this tool. I would like to know if the CHEUI model can be applied to SARS-CoV-2? I have obtained the result of solo outputs using...

A problem in the PositionalEncoding model code

3

Hi， Thank you for developing Corigami ! I have encountered some problems when I use corigami to train my data.  After the encoder step，here, the transposed matrix is input...

How to construe rna004 model [email protected]_DRACH bedMethyl output?

2

Hi, I have successfully run Dorado with RNA004 m6A model and used modkit to convert my modbam file to bedmethyl output. `${DoradoDir}/dorado basecaller --min-qscore 7 --verbose --emit-moves -k 14 --secondary=no...

Gets all reads key error with dorado

10

Hi, I encountered an issue when using buttery-eel to baseclling with dorado-server.  I want to use Dorado to basecall the RNA methylation model. Here is my code: ` Slow5Dir="/public2/hjliang/ONT_data/slow5"...

pod5 merge hangs indefinitely at 99-100%(the last 20 pod5 have not been merged)

5

## Issue Description > I use pod5 merge to merge my pod5 file, I have 3320 pod5 files. It seemed to have stopped processing the last 20 pods. However, nohup...

modkit extract m6A tsv problems

9

Hi, @ArtRand I encountered some issues while using modkit extract. Here is my code: `${modkitDir}/modkit extract ${bamfile}/input_merge_sup_m6A_pseU.mod.sorted.bam null --read-calls ${bamfile}/input_merge_sup.pass.m6A.reads.tsv --reference ${index_dir}/gencode.vM33.normal.transcripts.fa --motif DRACH 2 --log-filepath ${bamfile}/input_merge_sup_m6A.reads.log --mapped-only -q 10000...

Can f5c eventalign output base calling sequences ?

32

Hi @hasindu2008 , Thank you for developing f5c ! I wonder know whether f5c eventalign can output basecalling kmer? Generally, f5c eventalign will output the following header files. contig position...

Too few arguments for '--mm2-opts'

1

# Issue Report ## Please describe the issue: When I running dorado basecaller , I encountered the following error.  ## Steps to reproduce the issue: My dorado basecaller code:...