Hello! I am doing DESeq2 for the first time. A bit of background: I am downloading the already public data available from ENA browser. I have been able to successfully do Kallisto on the paired reads. The output of such files in in .tsv format. I am really confused on how to proceed with DESeq2 after this? I do have the set parameters for the log2 count and probability. I have 6 samples: 3 replicates of treated condition and 3 replicates of the controlled condition.

Can someone pls hep me out, i am really lost on how to give it a start. Does anyone have a pipeline they are willing to share? It will help me a bit!

First step: Use tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto_with_TSV_files

Second step: Use DESeqDataSetFromTximport from the DESeq2 package

Many answers to this question exist on these forums: e.g. tximport, Kallisto and Deseq2 (quick answer)