High scoring segment pairs
rehab-fouad opened this issue · 5 comments
rehab-fouad commented
How to calculate high scoring segment pairs with minimap2 for nanopore cDNA reads?
lh3 commented
What do you mean by "high scoring segment pairs"? What do you want to do?
rehab-fouad commented
I want to know the length and numbers of segment in per read that mapped to the reference without gaps or mismatches
lh3 commented
Sorry. You can't do that with minimap2.
rehab-fouad commented
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
or which tool I can use to get this value from minimap output file?