Open aakashsur opened 5 years ago
Glad that you have finished all the steps in mHiC. Yes, after mHi-C processing, you will need to do a filtering based on your own needs. We recommend filter the probability column (6th) column by >0.5 so that each multi-read can have at most one selected alignment position. You can also do >0.6 or >0.9 for more stringent filtering. Then merge with your uni-reads bin-pair count file and get the interaction counts for each bin-pair. You will need to write your own code but it can always be done by a few shell commands. I can add a few recommended commands to the manual later.
So after step 6, is there a way to go from the output file:
To a count format where the multi-mapping reads have been assigned to the highest probability location?