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novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
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biological/technical replicates #87

Closed LeilyR closed 3 years ago

LeilyR commented 3 years ago

Hi,

Thanks for the great tool. I am a newbie in the field of RNA modification and would apreciate your guidence on any recommended number of biological/technical replicates which your tool needs to to retrun the optimal output. (I have ko and wt of mouse)

Best, Leily

Huanle commented 3 years ago

Hi @LeilyR,

Apologies for the late response.

As in the case of differential gene expression analysis, there is a general consensus that increasing the number of samples will increase the statistical power of the relevant analyses. However, recommendations for the number of samples always vary according to different studies. The interplay between the number of replicates, reads alignment, sequencing depth, and other factors will further complicate the issue. So I do not have an idea of the ideal number of replicates for your study. That said, at the lower end of my recommendation, if the budget permits, it will be good to have 3 replicates, which is the median of the number of replicates used in DGE studies.

Huanle

LeilyR commented 3 years ago

Hi @Huanle,

Thanks a lot for the reply. We were also thinking of 3 reps. for that same reason. Good to hear that this would technically be suffficient to use your tool.

Cheers, Leily