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alexdobin / STAR

RNA-seq aligner
MIT License
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Mapping PE RNAseq reads to error prone Nanopore genomic reads #1022

Open chocotwig opened 3 years ago

chocotwig commented 3 years ago

Hi, For our application, we wish to map NGS RNAseq (Illumina PE) to long error prone Nanopore genomic reads. Could you please suggest some settings that we could adapt to make STAR capture these mappings better? We're assessing the total genic space contained within the nanopore long reads.

Some settings I use: --outFilterMismatchNmax 50 \ --outFilterMismatchNoverReadLmax 0.15 \ --alignIntronMin 20 \ --alignIntronMax 1000000 \ --alignMatesGapMax 1000000 \

Thanks!

alexdobin commented 3 years ago

Hi @chocotwig

I do not think STAR (presently) will work well for such purpose, as the error rate will probably be too high. I think you are better of using minimap2.

Cheers Alex