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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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How does "-s" parameter affect the alignment results? #1165

Closed kerenzhou062 closed 6 months ago

kerenzhou062 commented 6 months ago

Dear Heng,

I'm currently using minimap2 to align Nanopore cDNA reads to the human genome using following parameters: minimap2 -ax splice -Y -s 40 --secondary=no --junc-bed

I noticed that, the supplementary alignments will increase when changing -s 40 to -s 0. I'm curious about how -s affect the alignment results, especially the supplementary alignments. And do you have any suggestions on how to improve the supplementary alignments for short clipping reads (soft clip length < 40nt)?

Thanks,

Keren

lh3 commented 6 months ago

how -s affect the alignment results

Drop alignments if scores lower than -s

any suggestions on how to improve the supplementary alignments for short clipping reads (soft clip length < 40nt)

Adding -n2 -m20 might help, but generally minimap2 is not the right tool.