With bulk-RNA I am used to using STAR-RSEM (gene-level)-tximport-DESeq2 as a standard workflow; it is well documented and via tximport the effective_length from RSEM is also 'taken into account'. Now, I am working with scRNA and I am getting confused with how to import the RSEM counts for analysis; looking at the source-code of tximport, I don't see the effective_length being used for anything other than just being included as a variable in the resulting object.
I would like to know when, where and how is the effective_length information from RSEM incorporated? How/if this benefits scRNA, or what is the advised way of using RSEM count estimates in single-cell RNAseq?
data: full-length data; smart-seq2
I am very grateful for any input on this, thanks!