Table 4 Number of genes with B73 and Mo17 positively acting, cis-regulatory alleles detected in different analyses
From: Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias
Methods | STAR-StringTie | TopHat2-Cufflinks | Salmon | ||||
|---|---|---|---|---|---|---|---|
cis-eQTL only | default criteria | relaxed criteria | most relaxed criteria | default criteria | relaxed criteria | most relaxed criteria | default criteria |
Total | 9306 | 9256 | 9260 | 11,908 | 11,720 | 11,643 | 7855 |
B73 positive cis-eQTL | 6341 (68.1%) | 6203 (67.0%) | 6172 (66.6%) | 9905 (83.2%) | 9639 (82.1%) | 9504 (81.6%) | 4959 (63.1%) |
Mo17 positive cis-eQTL | 2965 (31.9%) | 3053 (33.0%) | 3088 (33.3%) | 2003 (16.8%) | 2081 (17.8%) | 2139 (18.4%) | 2896 (36.9%) |