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Improved correct command and assignment of multimapping reads

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@pmelsted pmelsted released this 07 Nov 07:04
· 309 commits to master since this release

This release improves the memory footprint and speed of the correct command of bustools.

The bustools count command adds the --em option that estimates gene abundances using an EM algorithm for reads that pseudoalign to multiple genes.

Note that the --multimapping option splits the read counts evenly across all genes, whereas the EM algorithm gives a more statistically valid answer. The two options are mutually exclusive.