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a-slide / NanoCount

EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
https://a-slide.github.io/NanoCount/
MIT License
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Why NanoCount needs sorted alignments? #20

Closed callumparr closed 1 year ago

callumparr commented 1 year ago

Out of interesting question because salmon actually recommends not having alignments sorted, so was wondering why the difference. Both are forms of maximizing expectations so is there ar reason having sorted alignments is better than unsorted?

josiegleeson commented 1 year ago

From my understanding, it just speeds up the process to have them sorted. NanoCount will run on unsorted bam files it just takes a little longer. Unsure for salmon though, it might be required for it to run or something to do with short read alignments which it is designed for?

callumparr commented 1 year ago

Thank you for the explanation