I have scRNA seq data downloaded from GEO.
Objective- I want to see gene abundance for my gene of interest - X-gene in cancer in men and women.
Questions- a)What is the difference between gene and transcript and therefore will it be called gene abundance /transcript quantification or both the above terms are same?
b)For doing this do I have to download raw GSE files or GSM matrix,barcode... files?
c)This step is done before clustering or can be done after clustering?
d)What is the difference when we say differentially expressed gene in man and women or doing gene abundance or transcript quantification for gene X in man and women?
e)Can I know if a particular cell is expressing that gene more or less?
Please can you give example of a paper or analysis code where this has been done.
Thanks a lot in advance!