Downstream processing from nf-core/rnaseq before ML analysis

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

There are multiple count tables from nf-core/rnaseq, the best depends on your use case. I would personally use the Salmon pseudoalignment counts and import them with tximport into deseq2 or limma-voom. I wouldn’t transform the data before doing analysis, see discussions like this.

For a downstream analysis tool, try nf-core/differentialabundance

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