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 :
the tabular one is the input of Deseq,
when I run the DeSeq jobe, it’s returned with an error!
hi @gallardoalba ,
this is the error that i get , i tried the deseq in the last days with different sources of reference transcriptome and annotation files, i got the same error.