Kallisto Bootstrapping and deseq2

Kallisto Bootstrapping and deseq2


Dear all,
Just a quick clarification about importing pseudocounts into the deseq2 package. I don’t usually apply the bootstrapping step with the Kallisto package for deseq2 analysis. My results are definitely comparable to ones generated by technicians in my university with totally different approaches. Nevertheless, my question is whether it could be considered a mistake not to run the pseudoalignment step without the bootstrap part when the tsv files are then processed by the tximport package for the downstream analysis with deseq2. Thanks



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