Hi, I've started learning RNA-seq only recently. I use nanopore technology(cDNA sequencing) for finding novel transcripts. But I don't know exactly which analyze tools are suit for this. I read several papers about this but I couldn't fully understand.
For example, I wanted to visualize my sequencing data with IGV. But IGV only take mapped sequencing data, which exclude novel transcripts(as I know...). And when I use Gffcompare, I cannot extend my analyze with data categorized as "u".
These several lack of my knowledge makes me confused. So, is there patterned pipelines for finding novel transcripts using informatics before doing actual verification such as RT-qPCR, cloning, and so on...?
And, thank you for all of you! every question and answer was very helpful for my studying.
Do you have a reference genome available? If so, reads from novel transcripts should still be mapped.
Yes, I used minimap2 with GRCh38.p13.genome. Honestly, I have difficulty to choose reference genome and annotation. How can I choose genome version compatible with my analyze plan? Until now, I followed genome version used in papers.