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nextflowrna-seq

nf-core/rnaseq not running deseq2 analysis

i'm running the nf-core/rnaseq pipeline and it finished ok, but it doesn't do the deseq2 comparisons or pca plots. I've used version 3.5 and 3.10.1 of the pieline and neither do the differential analysis. I'm using Hisat2, is this differential analysis only for salmon?

Thanks

Solution

  • TL;DR; Use --pseudo_aligner salmon option to run DESeq2 in addition to --aligner hisat2.

    Assuming you don't use the --skip_qc or --skip_deseq2_qc options, nf-core/rnaseq v3.10.1 will only perform a differential expression analysis using DESeq2 if using --aligner star_salmon1 (which is the default aligner) or using --aligner star_rsem2. DESeq2 is not run when when --aligner hisat23 is used alone. You can, however, run DESeq2 by specifying the --pseudo_aligner salmon option to run DESeq24. This option runs in addition to --aligner.