Supplementary Figure 2: GIREMI performance using a different read-mapping and variant-calling method (BWA mapping and GATK variant calling; see Supplementary Note 2).
From: Genome sequence–independent identification of RNA editing sites
(a) GIREMI results using reads processed by BWA and GATK. Numbers of predicted RNA editing sites by GIREMI in the GM12878 lymphoblastoid cells (ENCODE, cytosolic, polyA+ RNA-seq) are shown. Different fractions of genetic SNPs of GM12878 were assumed as unknown by excluding them from dbSNP. For each fraction, the SNPs were selected randomly. The percentage of GM12878 SNPs (based on genome sequencing data) among all single-nucleotide mismatches identified in the mapped RNA-seq reads after filtering for artifacts is shown (input data, gray bars, see Methods). The percentage of false positives (GM12878 SNPs) among all predicted editing sites is shown as orange bars. The total number of predicted editing sites and percentage of A-to-G editing are shown (numbers in orange). (b) GIREMI results using reads processed by the stringent mapping pipeline (Online Methods), shown for comparison purpose. The results are the same as in Fig. 1c.
