Table 6.

Overview of the seven mappers used in this study.

Mapper	Version	Parameters	Reference
bwa aln	0.7.13	Default	Li and Durbin (2009) [11]
CLC	9	Default	Qiagen, Hilden, Germany [41]
kallisto quant	0.42.5	--single, -l 150 and -s 25	Bray et al. (2016) [16]
HISAT2	2.1.0	Default	Kim et al. (2019) [19]
RSEM	1.2.30	--bowtie2, --fragment-length-mean 150 & --fragment-length-sd 25	Li and Dewey (2011) [14]
salmon quant	0.6.0	--type quasi, -k 31 --fldMean 150, --fldSD 25 and -l SF	Patro et al. (2017) [15]
STAR	2.5.2a	--outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --alignSJDBoverhangMin 8 --outSAMunmapped Within --quantMode TranscriptomeSAM GeneCounts	Dobin et al. (2012) [12]