Cycling conditions for Index PCR might need to be optimized per sample to obtain a final library that falls within ~50-200 nM. For nuclei derived from FFPE blocks, we typically use 1-2 additional cycles during indexing to start with. If the library does not reach the recommended range but the Bionalyzer/Fragment Analyzer/Tapestation traces look as expected (single peak at ~265 bp), then do not add additional cycles. If you see signs of under/over amplification in the traces, then adjust cycling accordingly.