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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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Finding overlaps between long RNA reads #434

Closed PengNi closed 5 years ago

PengNi commented 5 years ago

Hi Heng,

Can minimap2 be used to find overlaps between long RNA reads (e.g. PacBio Iso-seq, Nanopore 2D cDNA-seq and Direct RNA-seq reads)? Should I consider splice/junctions when I do this?

Thank you in advance! Peng

lh3 commented 5 years ago

You should not consider junction motif. The preferred setting depends on your goal. Do you want to cluster different isoforms or not?

EDIT: fixed a typo

armintoepfer commented 5 years ago

Fwiw, I don't consider junction motifs in IsoSeq3 cluster.

PengNi commented 5 years ago

@lh3 , I just intend to use pairwise alignment to do self-correction of the raw reads.

lh3 commented 5 years ago

@PengNi I think you can use a setting similar to IsoSeq3. @armintoepfer what setting are you using?

armintoepfer commented 5 years ago

Just use defaults with -k 15 -w 5. Make sure you don't cluster anything that has larger gaps.

PengNi commented 5 years ago

Okay, thank you. I'll have a try.