The Cell3 Target protocol suggests using 16 cycles for targets <0.04Mb. My targeted region is very small <0.01Mb. Should I still only conduct 16 cycles of post capture PCR?

Section 2C, Captured library amplification, of the Cell3 Target protocol gives general guidelines on the suggested number of post capture PCR cycles. For very small targets the number of cycles would need to be increased. For example, 0.004Mb may need an additional 2 cycles (total 18) to ensure there is enough library for sequencing. Therefore, please note that for very small targets you may need to optimise the number of post capture PCR cycles.