Hi,

This might be a very simple question but I am new to bulkRNAseq and would like to analyze paired FastQ files with DESeq2, rnaseqGene, or edgeR. Could anyone provide me with some simple code to get started? I would be happy to use any of the packaes. It seems like the first step is to convert the files to .txt files, which I can't figure out how to do.

Our lab uses Salmon, tximport or tximeta, and then DESeq2.

A workflow is here:

https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#preparing-quantification-input-to-deseq2