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UMI Model Clarification #61

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asistradition opened this issue Aug 19, 2020 · 0 comments

asistradition commented Aug 19, 2020

My workflow for using kallisto on single-cell data is:

kallisto bus
bustools correct
bustools sort
bustools count --genecounts

How exactly are UMIs modeled when counting transcripts/genes in this workflow?

Are sequence-adjacent (Hamming distance of 1) UMIs merged together? Is this transcript-specific or is there any merging of adjacent UMIs that map to different genes?
Is there any thresholding for number of observed UMI & transcript pairs or is one read enough to count?
Does this behavior depend on anything that can be set at runtime? Either explicitly or implicitly through changing the technology flag, etc?

Appreciate the help - kallisto & bustools are excellent pieces of software.
Thanks!

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