Long Ranger2.0, printed on 12/22/2024
Loupe requires and runs on .loupe files generated by the longranger pipeline. The Loupe file for a given sample can be found in the outs subfolder of the sample folder output by longranger.
Once Loupe is started, click on the open file button to select a Loupe file to load. You can load a different file at any time by clicking the Open Files... link in the upper-right corner of the window.
Loupe provides a search bar at the top of the window for genome navigation. The search bar accepts gene names or loci in chr:start-end format. Loupe supports multiple search ranges, separated by spaces, commas, or semicolons. Loupe will maintain the previously selected loci ranges (if possible) when switching between views. Valid searches include:
ELM4,ALK: view EML4 and ALKchr1:5000000: display region around chr:5000000chr1:5000000,BRCA1,chr3:7000000-8000000: display regions from three chromosomes: or +; or ,chrXX: or chrXX+ will be interpreted as a gene