Kallisto bustools index


I am trying to build an index for a single nuc experiment using Kallisto, but I was wondering if someone could please help breakdown the following for kb ref

I am a bit confused on what exactly the significance of t2g.txt, cdna_t2c.txt, and intron_t2c.txt are

I am also not 100% sure about the difference between lamanno vs nucleus on the workflow

kb ref -i index.idx -g t2g.txt -f1 cdna.fa -f2 intron.fa 
-c1 cdna_t2c.txt -c2 intron_t2c.txt --workflow lamanno -n 8 
Mus_musculus.GRCm38.dna.primary_assembly.fa.gz Mus_musculus.GRCm38.98.gtf.gz




updated 38 minutes ago by


written 17 hours ago by


You want to feed those files into kb count

Briefly, t2g.txt contains the transcripts-to-gene mappings, cdna_t2c.txt contains all the cDNA (spliced) transcripts, and intron_t2c.txt contains all the "intronic" (i.e. unspliced) transcripts.

nucleus is used for single-nucleus data while lamanno is used for RNA velocity. There are subtle differences between the two workflows (e.g. for nucleus, the spliced+unspliced matrices are added up while for RNA velocity, separate matrices are generated that can be fed directly into the velocyto workflow).

before adding your answer.

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