Mapping transcripts to nanopore genomic reads

[chocotwig]

Hi, I use the following command to map transcripts to my individual nanopore genomic reads:

./minimap2-2.17_x64-linux/minimap2 -c -x map-ont -G4000 -F4000 -g4000 -r4000 --hard-mask-level -M 0 --secondary=no -uf -C5 transcriptome.fa nanoporeLongReads.fastq > output.paf I realise that the target-query order in the command is flipped around. But I only want a maximum of one best annotation for each position on the long read. Do you think that this command is okay?

I have tried using other evidence-based annotation tools, but these typically give me multiple spliceforms, etc. Thanks very much! Really appreciate your help.

[lh3]

I am not sure about your purpose. If you just want to find local hits, use minimap2 -cx map-ont transcriptome.fa reads.fa should be adequate.

[chocotwig]

Okay! Thanks - could you explain what you mean by local hits? Hits for individual reads one at a time, as opposed to the entire genome dataset altogether?

Thanks!