Current best practice for alignment and quantification for downstream analysis in DESeq2

Question

[yura.grabovska]

Looking at the nf-core/rnaseq pipeline, the alignment and quantification tools that are available are STAR+Salmon, STAR+RSEM and HISAT2. I've not had to deal with bulk RNASeq data for a while so I'm wondering what is the consensus for getting raw counts out for DESeq2. In the past I ran STAR+htseq-count but that doesn't seem to be an option avialable from the pipeline which makes me wonder if it's because it's old and not the best way to do things any more.

Answer 1

[Devon Ryan]

htseq-count was effectively replaced by featureCounts and more recently that's largely (but not entirely!) been replaced by using salmon. So STAR+salmon or even just salmon alone would generally be best, assuming you have a well annotated transcriptome.