I am very new to galaxy. I have CNV call data which has a start position and stop position for the genomic region of variation. What I want to do is pull out the genes that over lap these probe position, but unclear on how to do this.
The tools in the groups "Operate on Genomic Intervals" and "NGS: BED Tools" will intersect two datasets of genome coordinates. Obtain the reference annotation for genes/transcripts from UCSC, Ensembl, Biomart, etc.
It is important that the reference genome associated with your calls and with the reference annotation are an exact match, and that both exactly match the reference genome used in Galaxy. Here is how to check: