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lh3 / minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences
https://lh3.github.io/minimap2
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Whether positive/negative strand should be considered when direct RNA sequencing reads are mapped to transcriptome? #474

Closed weir12 closed 5 years ago

weir12 commented 5 years ago

Hi Heng :

Whether positive/negative strand should be considered when direct RNA sequencing reads are mapped to transcriptome(cDNA)?In my view, cDNA library is produced by reverse transcription of mRNA.So each cDNA sequence is like a template strand in genome.However,the result of minimap2 shown mappings to both reverse strand and forward strand.

Thanks!

lh3 commented 5 years ago

What do you mean by "transcriptome"? Annotated genes or sequencing reads? If the former, on positive strand only; if the latter, both strands.