Kallisto quant & Kallisto pseudo

what is the differences between this two tools, and which one i should use for pseudoalignment.
after alignment which tool can i use for normalization?

Hi @azzahrae,

you should use Kallisto quant; Kallisto pseudo runs only the pseudoalignment step and is meant for usage in single-cell RNA-seq. If you want to perform a differential expression analysis you do not need to normalize it . You can feed DESeq2 with the output generated by Kallisto.

Regards

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thank you so much.
I have another question please; Kallisto generate 3 output :
image
the tabular one is the input of Deseq,
when I run the DeSeq jobe, it’s returned with an error!
image

Hi @azzahrae,
could you share the error report? You can find it in that way:

Regards