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lh3 / miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)
MIT License
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High scoring segment pairs #40

Closed rehab-fouad closed 6 years ago

rehab-fouad commented 6 years ago

How to calculate high scoring segment pairs with minimap2 for nanopore cDNA reads?

lh3 commented 6 years ago

What do you mean by "high scoring segment pairs"? What do you want to do?

rehab-fouad commented 6 years ago

I want to know the length and numbers of segment in per read that mapped to the reference without gaps or mismatches

lh3 commented 6 years ago

Sorry. You can't do that with minimap2.

rehab-fouad commented 6 years ago

at the link you sent me about fap https://lh3.github.io/minimap2/minimap2.html#10 there is a description of ms; which is the maximum scoring segment. but in the output file, I got I don't get this column. do you have any idea how can I get this?

rehab-fouad commented 6 years ago

or which tool I can use to get this value from minimap output file?