-
Notifications
You must be signed in to change notification settings - Fork 28
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
technical replicates #220
Comments
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? |
Thanks- we'll consider taking matrices with unmerged tech reps in future development. |
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
The text was updated successfully, but these errors were encountered: