Response to Comments on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome”

Kleinman and Majewski, Pickrell et al ., and Lin et al . suggest that mapping and sequencing errors and genetic variants led to false discovery of RNA-DNA sequence differences in our paper. We repeated our analysis using two different sequence alignment methods and carried out additional experiments including whole genome DNA sequencing. The results are consistent with our finding of widespread RNA-DNA sequence differences.