Quality check pipeline for PCR cDNA ONT sequencing output.

Question

[Sbrillo]

Hi all,

I was looking for a solid workflow to perform quality checks on long-read RNA sequencing data using the ONT PCR cDNA kit.

I was surprised that many people/groups adopt different methods or tools, and there isn't a straightforward methodology yet.

Before performing Transcriptome assembly, quantification or running isoform discovery tools (such as Isoquant), what tools do you suggest for adapter trimming, strand orientation, and read correction for this type of sequencing output?

My case involves using ONT PCR cDNA data to look for novel transcripts/genes and improve the current annotation. Any other suggestion for quality checks for Denovo transcriptome assembly would be appreciated.

Thanks in advance for the help

Best

Answer 1

[GenoMax]

ONT provides a workflow for working with transcriptomic data: https://github.com/epi2me-labs/wf-transcriptomes

Assuming dorado has been used for basecalling with appropriate "kit" information (if samples are multiplexed) then adapters should already be trimmed. You can use dorado correct to do read correction.