Hi! After reading the documentation, I still do not fully understand what is the difference between transform_counts() and compute_read_counts() of the recount3 package. If anyone can help me clarify this I would really appreciate it :)

I was planning to run this code to get the counts so that afterwards I will be able to run a machine learning analysis. Do these steps make sense?

#  Step 1:Coverage counts--> read counts
    assay(rse_gene_object, "counts") <- transform_counts(rse_gene_object)

# Step 2 :read counts---> counts matrix
    counts<-compute_read_counts(rse_gene_object)

Thanks!

Hi @fdelillo,

If you are used to working with read counts, I suggest you use compute_read_counts() only. In terms of the documentation, I'd appreciate more specific feedback since we tried to talk about all the different options we have. There's also https://f1000research.com/articles/6-1558 from the recount2 project that explains more details about the concept of base-pair read counts.

Best, Leo