I am using kentUtils bedToPsl inorder to convert a bed file to psl file inorder to map the results using pslMap.
There is an option in bedToPsl -keepQuery
Their documentation says :
-keepQuery - instead of creating a fake query, create PSL with identical query and target specs. Useful if bed features are to be lifted with pslMap and one wants to keep the source location in the lift result
I am trying to understand how this can help and tested the difference with and without keepQuery but I couldn't really understand. Please if anyone can help me with it I would be grateful.