technical replicates about differentialabundance HOT 3 OPEN

Thanks- we'll consider taking matrices with unmerged tech reps in future development.

from differentialabundance.

Assuming this is RNA-seq, we would normally expect technical replicates (assumed to mean multiple sequencing runs of the same biological sample) to have been collapsed in the upstream analysis- see https://nf-co.re/rnaseq/3.13.2#usage.

Do you have reason to handle individual tech reps separately?

The DESeq2 module in nf-core doesn't currently have capability for collapsing the tech reps there, so that would need addressing before we could handle them as part of this workflow.

from differentialabundance.

Thanks @pinin4fjords for the response. I just wanted to see how well the tech-reps are clustering and they were clustering quite well 👍🏽 So i tried to merge the counts by summing and presented the sum of tech-reps as bio-rep in contrast for RNA-seq pipeline, which seems to have worked 🤞 Probably this process can be part of pipeline itself?

from differentialabundance.