direct RNA long-reads alignment against reference genome

Question

[frarodmar17]

I am analysing Nanopore direct RNA-seq data and I am a bit confused. I have to align the RNA reads against a reference genome with minimap2 but direct RNA fastq files contain RNA reads and not cDNA. Can I align these reads against a reference genome directly? I guess it depends on library type, if reads are forward-stranded or reverse-stranded.

Answer 1

[GenoMax]

Can I align these reads against a reference genome directly? I

Yes you can with the following pre-set as noted in minimap2 quick guide.

./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam  # noisy Nanopore direct RNA-seq

More details here:https://github.com/lh3/minimap2?tab=readme-ov-file#map-long-splice

[frarodmar17]

Okay, thanks! I removed reads.fa and I used the index created with minimap2 in .mmi format. Is this correct?