RES-Scanner: a software package for genome-wide identification of RNA-editing sites

GigaScience

Table 2 Comparison of the cumulative CPU times (hours) for RES-Scanner, REDItools and GIREMI in processing the human GM12878 dataset from pre-aligned reads to final editing sites

Chromosome	RES-Scanner	REDItools	GIREMI
chr1	39.71	118.98	ND
chr2	44.51	128.62	ND
chr3	37.95	106.15	ND
chr4	29.83	81.61	ND
chr5	31.16	88.89	ND
chr6	28.99	85.49	ND
chr7	25.60	82.45	ND
chr8	25.38	64.02	ND
chr9	20.23	63.79	ND
chr10	23.01	71.45	ND
chr11	20.80	68.59	ND
chr12	23.33	75.51	ND
chr13	14.65	40.37	ND
chr14	16.10	51.55	ND
chr15	14.82	48.73	ND
chr16	15.64	48.15	ND
chr17	14.54	54.50	ND
chr18	13.03	35.29	ND
chr19	13.07	31.63	ND
chr20	12.19	31.04	ND
chr21	7.59	15.66	ND
chr22	7.67	21.62	ND
chrX	21.80	60.09	ND
chrY	1.62	1.94	ND
Total	503.23	1,476.12	10.87

Note: A total of 150 Gb of pre-aligned DNA reads and 9 Gb of pre-aligned RNA reads in BAM format were used as inputs for both RES-Scanner and REDItools, while 9 Gb of pre-aligned RNA reads and a list of SNVs derived from the RNA-seq data were used as inputs for GIREMI. The time for GIREMI included the cumulative CPU times of generating the SNV list from the RNA-seq data using SAMtools [40] (9.60 h) and running GIREMI (1.27 h). As GIREMI required all SNVs from the whole genome to construct the MI distribution, CPU times for individual chromosomes could not be determined. ND not determined

ISSN: 2047-217X