Figure 8.

Sources of artifacts in Class I, II and III techniques. Left: Identification of RT-signatures in Class I methods may be affected by the presence of genomic SNPs, by possible mis-aligned nucleotides at exon-intron borders and by errors in the sequencing data set. Center: Class II approaches may generate false-positive signals due to strong non-specific cleavage sites in RNAs, due to mis-alignment of some reads to repetitive RNA sequences, due to unannotated transcription sites. Right: Class III approaches based on Ab enrichment may suffer from non-specific enrichment signals, from Ab promiscuity or mis-alignments. Important controls for these approaches include the coverage profile in the input (top trace), and the enrichment profile for KO or deleted strain (middle). Only specific peaks present in WT sample and absent in control traces should be considered as candidates. The insert shows that the position of the modified residue does not always correspond to the maximal enrichment.