2. User Guide

• Start RicePilaf by visiting http://localhost:8050/ on your browser (if installed locally) or by visiting any of the sites where RicePilaf is being served.

• You will be greeted by the following screen.

  

• In the input box, enter genomic intervals like so: Chr01:100000-200000. Multiple intervals should be separated by a semicolon like so: Chr01:100000-200000;Chr02:300000-400000. These intervals are obtained from LD-based clumping of significant GWAS SNPs or from QTL mapping studies.

• Once you click the "Proceed to Analyses Menu", a menu appears as a sidebar on the left.

  

• Each analysis type has its a dedicated user guide you can find from the sidebar of this wiki.

• You can perform the analyses in any order, but it is recommended to go from top to bottom in sequential order.

• The Reset All Analyses button clears the display of all the results you might have obtained and takes you to initial state of the app.

• The Clear Cache button deletes all temporary and intermediate files that were generate by your analyses.