This may sound similar to my previous questions, but I am confused and have many more questions.
How can I download ALL genes from Ensembl/Biomart websites? (or use mysql?)
I can also download Ensembl genes from UCSC; so what's the difference between Ensembl genes from Biomart and UCSC?
I compared refseq gene(from UCSC genome browser) and Ensemble gene(from UCSC genome browser). The coordinates cat be slightly different (maybe a few hundred bp away). Will this lead to confusion? Basically I wanna find the overlapping regions between the identified structural variants and genes. I'm using g1k_37v as reference for alignments. So which gene lists should I use? refseq or ensembl?