Inquiry Regarding Basecalling Parameters for Transcript-Level Methylation Analysis

[Taylorain]

Dear Dorado Development Team,
I am currently working on transcript-level methylation analysis and am considering aligning drs reads to a reference transcriptome while basecalling. I have a few questions regarding the appropriate parameters and methods for this approach. The reference transcriptome was assembled using the same drs data.

1. Basecalling Alignment to Reference Transcriptome:
   • Is it feasible to align basecalled reads directly to a reference transcriptome using Dorado?
   • If so, which basecalling parameters are recommended for this purpose? Specifically, I am considering using the -x map-ont preset. Is this suitable for aligning to a transcriptome? But it coudn't work
2. Recommended Presets for Accurate Long Reads:
   • I understand that the -x lr:hq preset is recommended for accurate long reads with an error rate below 1%. Is this preset appropriate for aligning to a reference transcriptome, or is there a more suitable preset for this purpose?
3. Differentiating Methylation Modifications Across Transcripts:
   • Given that a single gene can have multiple transcripts, are there specific methods or tools within Dorado to distinguish methylation modifications at the transcript level?

I would greatly appreciate any guidance or recommendations you can provide on these topics.
Thank you for your assistance.

Best regards

[HalfPhoton]

Hi @Taylorain,
This technical bioinformatics question is best asked on the Nanopore Community Forum where there is better support for these types of questions.

Kind regards,
Rich