Table 1. The comparison of the hit numbers in 121 experimentally validated Arabidopsis MTIs between CleaveLand4 and StarScan.
| Parameter values 1* | Parameter values 2** | |||||
|---|---|---|---|---|---|---|
| GSE accession | Tissue | Treatment | CleaveLand4 | StarScan | CleaveLand4 | StarScan |
| GSE11007 | inflorescence | dT primer | 30 | 31 | 17 (1) | 16 (8) |
| inflorescence | random primer | 53 | 62 | 31 (3) | 35 (6) | |
| seedling | random primer | 55 | 56 | 27 (2) | 31 (5) | |
| GSE11094 | inflorescence | control | 89 | 91 | 66 (15) | 76 (70) |
| inflorescence | xrn4 mutant | 96 | 100 | 70 (17) | 82 (59) | |
| GSE47121 | flower bud | rep A | 71 | 76 | 43 (8) | 50 (26) |
| flower bud | rep B | 71 | 76 | 43 (9) | 52 (22) | |
| GSE52342 | inflorescence | control | 60 | 65 | 47 (12) | 45 (20) |
| inflorescence | ddm1-2 mutant | 85 | 88 | 47 (12) | 61 (49) | |
| inflorescence | ddm1-2 & rdr6-15 mutant | 79 | 86 | 54 (13) | 60 (33) | |
| inflorescence | rdr6-15 mutant | 80 | 83 | 53 (14) | 52 (26) | |
| GSE55151 | leaf (early senescence) | rep 1 | 86 | 88 | 55 (15) | 72 (59) |
| leaf (early senescence) | rep 2 | 74 | 79 | 50 (13) | 58 (60) | |
| leaf (late senescence) | rep 1 | 38 | 38 | 22 (7) | 18 (8) | |
| leaf (late senescence) | rep 2 | 46 | 46 | 29 (4) | 27 (23) | |
| leaf (mature) | 91 | 97 | 55 (24) | 74 (98) | ||
| leaf (young) | 95 | 99 | 54 (28) | 75 (107) | ||
| All | All | 105 | 110 | 89 (60) | 90 (215) | |
*: Default parameters (no P-value filtering and all categories reported) in CleaveLand4. **: Default parameters in StarScan. Detailed options of StarScan: FDR < 0.01, category = 0–2, cleavage site = 10, RPM > 0.1, penalty score < = 5, stringent mode, Bowtie-specific parameters ‘-a -v 0 -m 10’; Detailed options of CleaveLand4: P < 0.01, category = 0–2, cleavage site = 10, Bowtie-specific parameters ‘-v 1 - -best -k 1’. The numbers inside the parentheses represented the counts of other MTIs that did not belong to the reference set.