Hello, I have 2 biological replicates and would like to use them to recalibrate weights. I use the runChicago.R wrapper and would like to clarify if the below is the correct (and most efficient) workflow:
- Run separately runChicago.R on each of the 2 replicates, that is two runs: in one run the input is only rep1.chinput and in the other run the input is only rep2.chinput
- Get the 2 separate rds objects, rep1.rds and rep2.rds and run fitDistCurve.R with --input rep1.rds,rep2.rds
- Update the settings File with the new weights from (2)
- Use the updated settings File to do one more run of runChicago.R this time providing the comma-separated list rep1.chinput,rep2.chinput
Also, if the above is valid, can you advice on whether the attached diagnostics indicate that the estimates from (2) are reliable?