Discussion: Change to always include introns? about scpca-nf HOT 4 CLOSED

I'm going to put this in the current Epic we have going just so it gets discussed alongside those issues.

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A note that we may also want to update alevin-fry reading code to use fishpond::loadFry(), which will simplify some of our code, and can allow us to keep multiple assays, should we so desire: I might propose counts (U + S + A), spliced (S + A), and unspliced (U); This would allow the greatest flexibility for downstream users, even enabling RNA velocity if people want to go that route.

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In looking into this, it appears that Space Ranger does not use introns automatically, and indeed that may not be possible, as I can't find an option in the docs. For Cell Ranger, the option is --include-introns, but that doesn't seem to exist in Space Ranger. So rerunning Space Ranger files may not be needed.

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Closing this in favor of #229

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