I am trying to retrieve gene information from ensembl website to compare the the gene information for mouse(mm10) with repetitive DNA is specific genome regions (UTR'S and intron, and upstream). I did two ways to get these files the first one using the R code below, and the second one by going directly to ensembl website using biomart tab to get these files.
I have 2 issues, the first one that there is a difference in total observations(rows) in both ways (i mean the total rows in both files are different).
The second issue, when I start find the genes that sharing the same position with these specific regions for repetitive DNA I got empty file results, and I don't know what causes that. BTW, I downloaded the repetitive DNA files from UCSC website using ensemble genes in track tab.
R code to retrieve the gene info.
Retrieving mouse (mm10/GRCm38) from Ensembl website
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")