search

nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
Other
545 stars 66 forks source link

Error in detection of modified bases in RNA sequecing by PromethION. #1156

Open shakti83kumar opened 2 days ago

shakti83kumar commented 2 days ago

Hi Evereyone,

I have RNA sequencing data that have been generated by PromethION. Screen shots of Run summary, Run configuration, Sequence output, Run health, Run log has been attached below. I want to find out RNA modified base "m6A" from the data. I run the program. but it is showing error. Please help me. Screenshot from 2024-12-02 16-24-12 Screenshot from 2024-12-02 16-24-20 Screenshot from 2024-12-02 16-24-29 Screenshot from 2024-12-02 16-24-44 Screenshot from 2024-12-02 16-24-51 Screenshot from 2024-12-02 16-29-03

juanjo255 commented 2 days ago

Hello @shakti83kumar !

I think probably is an error with syntax. When I'm basecalling using modified option, I do it this way: dorado basecaller --min-qscore 7 --trim adapters --modified-bases 5mCG_5hmCG --models-directory /path/to/models/ sup@v5.0.0 "$file" > Output.bam

Note the simplex model setting for model-directory then the modified-bases add the specificity.

I hope it helps!

malton-ont commented 2 days ago

@shakti83kumar,

dorado basecaller .../rna004_130bps_hac@v5.0.0_m6A@v1...

Your command is incorrect: the first model should be the canonical basecall model, not a modification model; modifications should be passed via the --modified-bases or --modified-bases-models parameters. Your command should look like:

dorado basecaller .../rna004_130bps_hac@v5.0.0 ... --modified-bases-model .../rna004_130bps_hac@v5.0.0_m6A@v1 > calls.bam

See the docs here for further examples.