Bulk RNA seq recommendation

[mdanb]

What do you recommend to try out for "big data" but for RNA seq instead of single cell?

[nhuhoa]

Hi,
RNA-seq means bulk RNA-seq? I think the best and also classical methods for bulk RNA-seq are ComBat or limma. I see another method that was particularly designed for bulk is Combat-seq but I never tried it before. You may want to test it.
https://github.com/zhangyuqing/ComBat-seq

From my point of view, bulk data is different from single cell data, and a good normalization method that allow to remove library size effects (sequencing depth, total read counts) is good enough to go.
Ex: using edgeR: https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

• combine all bulk samples into 1 data frame
• filtering genes with min_counts over all samples, filterbyExpr()
• compute library size
• calcNormFactors
• then convert normalized data to CPM table
• you may want to see more at: RNA-Seq of pathogen inoculated arabidopsis with
  batch effects https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
  in case you have many bulk samples

Have fun,
Hoa