Thanks, Alex! Sorry for my late reply as well. I was not notified that you have responded.
In general, how do you view soft-clipping for mapping short reads? For example, what happens if we don't trim all (short) adapters? Will it affect mapping quality? In our situation, we have two major issues:
- The 5' adapter removal might remove two-three bases from the 5' end of the read
- The 3' adapter removal might remove one additional base from the 3' end of the read
If we don't aggressively trim the adapters and allow soft-clipping, it seems more reads will be mapped.
Babak