Can I go from kallisto results to SEURAT directly

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3 months ago

biotrekker ▴ 100

Is there any thing else that needs to be done before I use SEURAT in R on my kallisto results. Am I missing a step. I heard about bustools but can't find more info on it. (Also this is single cell rna-seq data)

Thanks

cell bustoolls kallisto single • 442 views

ADD COMMENT • link updated 3 months ago by dsull ★ 6.8k • written 3 months ago by biotrekker ▴ 100

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If you already have matrix.mtx, genes.txt and barcodes.txt from kallisto output, you are ready to proceed into R for Seurat object creation.

library(Seurat)
?ReadMtx()

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ADD REPLY • link 3 months ago by bk11 ★ 3.0k

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Is their anything kallisto bustools that should be done first that I am unaware of? Because I get the three files you are mentioning after kallisto quant?

ADD REPLY • link 3 months ago by biotrekker ▴ 100

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Have you checked out the online tutorials? There are some older tutorials here: https://www.kallistobus.tools/ and a more recent one is here: https://www.biorxiv.org/content/10.1101/2023.11.21.568164v2.full.pdf

You'll need to show us exactly what your "kallisto results" are (i.e. what files you have) otherwise we have no idea what you're doing.

ADD REPLY • link 3 months ago by dsull ★ 6.8k

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