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tleonardi / nanocompore

RNA modifications detection from Nanopore dRNA-Seq data
https://nanocompore.rna.rocks
GNU General Public License v3.0
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control samples of replicates #149

Open LeilyR opened 4 years ago

LeilyR commented 4 years ago

Hi,

Is it alright if I use one ctrl sample for all the replicates of an experiment? Having replicates makes sense if the IVT goes on the same flowcell as its corresponding condition, right?

Best, Leily

a-slide commented 4 years ago

Hi @LeilyR Not necessarily actually. Running the same control sample on multiple flowcells will help to take the technical variability into account. You can use the same set of control condition technical replicates (IVT of KO) to compare against multiple experimental samples. When possible we recommend to use 3 replicates for each conditions. I hope this answer your question.

LeilyR commented 4 years ago

Hi @a-slide , thanks a lot. It was really helpful.

LeilyR commented 3 years ago

Hi, Just a very late follow up on this issue. If I have 3 biological rep. of wt and 3 biological rep. of ko., where no ko and wt were sequenced on a single flowcell (I do have technical bias). How would noanocomp treat each ko and wt sample since basically there no coresponding wt for each ko. Does this matter to the tool? Alternatively how much it helps the tool if i do have one wt corresponds to every single ko. From your previous answer I would say the tool works independent of it, but just to learn how it treats them. If eaiser maybe you can also point me to where in your code I can find the replicates handeling.