The TruSeq RNA and DNA v2 kits include adapters for 12 new indexes. RTA versions 1.12 and earlier cannot recognize these indexes and assign control reads from these indexes. To resolve this issue, replace the controls.fasta file on the instrument PC with this new version. This is only necessary for customers who are using TruSeq v2 DNA or RNA kits and sample prep controls. If customers are not using sample prep controls, RTA does not need to identify indexes. In this case, replacing the controls.fasta file is not necessary. Sample demultiplexing happens after RTA analysis and is not affected by this issue.