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not sure how to handle technical replicates in contrast file? i have a samples.csv like one presented at https://nf-co.re/differentialabundance/1.4.0/docs/usage but with one more column (tech) representing technical replicate
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.
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?
Description of the bug
not sure how to handle technical replicates in contrast file? i have a samples.csv like one presented at https://nf-co.re/differentialabundance/1.4.0/docs/usage but with one more column (tech) representing technical replicate
but i am not sure what should be the best way to present this information in
contrasts.csv?
Command used and terminal output
No response
Relevant files
No response
System information
No response
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