I have 2 biological replicates (Chip-Seq) and i want to know how to pool them together so that after pooling them together i may apply Homer to find peaks. I am doing it for the very 1st time thats y asking such a q.
Now my q is : I have found the peaks of replicates separately by Homer.
1.How to find the peaks higher than 1 read per million (rpm) from each replcate and then merge the peaks of replicates, So, how can I merge the peaks of replicates???????????????
2.Can I use Normalized tag count column to check for peaks higher than 1rpm.If yes,then what would be the interpretation of 145.7 normalized tag count. also what would be the value to check for >than 1rpm.
- how can i merge the peaks ?by mergeBed with -n option will be ok or not
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