The clock processing removes 8 bp of UMI (transferred to readID), and clips the following 5bp. In addition, 15bp are clipped off the 3' end, which takes care of the fill-in bias in RRBS experiments, however only for Read 1. We need to remove 2bp from the 5' end for Read 2 to get rid the fill-in bias at the start of Read2 (marked with B for biased):
In it's current implementation, the dual-UMI RRBS reads come in the following format:
The clock processing removes 8 bp of UMI (transferred to readID), and clips the following 5bp. In addition, 15bp are clipped off the 3' end, which takes care of the fill-in bias in RRBS experiments, however only for Read 1. We need to remove 2bp from the 5' end for Read 2 to get rid the fill-in bias at the start of Read2 (marked with
B
for biased):Resulting in: