Options for normalisation of RNA-seq

[frederikkemarin]

Description of feature

Hello,
Is it possible to normalise the RNA-seq counts in this pipeline? This is standard usage in many cases (e.g. the encode pipeline defaults to RPM normalisation).
Maybe this is already possible but I have simply missed it?

[davidecarlson]

Hi @frederikkemarin ,

TPM normalized counts are already produced as long as hisat2 is not chosen as the aligner. See the following output files:

salmon.merged.gene_tpm.tsv 
salmon.merged.transcript_tpm.tsv

You can also feed the results of this pipeline quite easily into the https://nf-co.re/differentialabundance pipeline to get counts normalized using DESeq2's median of ratios method.

Edit: changed "mediation" to "median."

[pinin4fjords]

Thanks @davidecarlson - that's a good response. Closing the issue.

[frederikkemarin]

Hey,
Thanks for the response, I was actually wondering about having counts per position normalised?