getting RNA-seq raw counts from Kallisto

Question

[Meghan.T]

Hi everyone,

I am using kallisto quant for RNA-seq data analysis. After running kallisto quant the output looks like this:

I am going to perform DEG analysis with DESeq2 and need raw counts, but the estimated counts are not integer values. Do you have any suggestions?

also posted on kallisto github: https://github.com/griffithlab/rnaseq_tutorial/issues/51

Answer 1

[GenoMax]

See answer from @dsull here: https://support.bioconductor.org/p/9156404/#9156407

[Meghan.T]

Great. Thank you very much!