JACUSA: site-specific identification of RNA editing events from replicate sequencing data
M. Piechotta, E. Wyler, U. Ohler, M. Landthaler, C. Dieterich (2017), JACUSA: site-specific identification of RNA editing events from replicate sequencing data, BMC Bioinformatics.
Analysis workflow to identify RNA editing sites in matched gDNA and cDNA HEK-293 samples. a Sequenced reads are mapped and PCR-duplicates are removed. b Single nucleotide variants are called for all sensible combinations of gDNA vs. cDNA and cDNA vs. cDNA BAM files
We present JACUSA, a versatile one-stop solution to detect single nucleotide variant positions from comparing RNA-DNA and/or RNA-RNA sequencing samples. The performance of JACUSA has been carefully evaluated and compared to other variant callers in an in silico benchmark. JACUSA outperforms other algorithms in terms of the F measure, which combines precision and recall, in all benchmark scenarios. This performance margin is highest for the RNA-RNA comparison scenario.
We further validated JACUSA’s performance by testing its ability to detect A→I events using sequencing data from a human cell culture experiment and publicly available RNA-seq data from Drosophila melanogaster heads. To this end, we performed whole genome and RNA sequencing of HEK-293 cells on samples with lowered activity of candidate RNA editing enzymes. JACUSA has a higher recall and comparable precision for detecting true editing sites in RDD comparisons of HEK-293 data. Intriguingly, JACUSA captures most A→I events from RRD comparisons of RNA sequencing data derived from Drosophila and HEK-293 data sets.
The code can be found at https://github.com/dieterich-lab/JACUSA.