How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
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4 months ago
mrj ▴ 70

I have RNA-seq read quantification results from Kallisto. Kallisto has output 1) estimated counts, and 2) tpm values. I am hoping to perform DESEQ2 analysis on these data. The DESQ2 documentation suggests that I should be using only count data as input. However, both of the Kallisto outputs are not discrete counts. They are continuous real numbers. What is the proper preprocessing to use Kallisto quantification tables on DESEQ2?

kallisto read DESEQ2 analysis counts differentialexpression • 711 views
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4 months ago

Use tximport to get your counts into DESeq2. It will understand how to do it properly.

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That is great! Thanks for this information, Swbarnes2

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4 months ago
Martombo ★ 2.9k

just round it up!

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Thank you Martombo

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