downstream analysis on the output of nf-core/rnaseq pipeline

Question

[r.shiasi3897]

Hello everyone, I ran nf-core/rnaseq pipeline successfully, now I want to do downstream analysis like machine learning on the generated output files from this pipeline. Should I use salmon.merged.gene_counts.tsv for that and apply log transformation to normalize it before doing downstream analysis?

Answer 1

[Trivas]

Depends what you're hoping to use ML for. But I would recommend using the tximport package and DESeq2 for easy pre-processing of your data.