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