Hi I need an information about the quantity of genes in each replicates how to do it
I am using two different types of mice WT and knock out, the samples for both types were taken at 5 different age groups and there are 3 replicates for each. my targets will be to get the differential expression which I think I know how to do it but I also would like to know the gene quantity of each replicate.
final results in cuffdiff does not show quantity of each replicates separately. it shows the genes quantity of the 3 combines replicates together in in two different types of mice.
can you give any suggestion please
Also how to convert the Galaxy gene id (TCONS- or XLOC_) into ensembl id
N.B. my samples are RNAseq (paired-end)