Table 2:

The criteria of basic and advanced filtering for four different types of input data for LeTRS

	Output filters​	Illumina paired-end amplicon reads	Nanopore amplicon reads	Nanopore dRNAseq reads	Bam
Basic filtering​	Mapping quality (MAPQ) >10​	● ​	● ​	● ​	● ​
	Read only one splicing junction ​	● ​	● ​	● ​	● ​
	Primary alignment only​	● ​	● ​	● ​	● ​
	No supplementary alignment​	● ​	● ​	● ​	● ​
	Read mapped in pair​	● ​	​	​	​
	No read reverse strand​	​	​	● ​	​
Advance filtering​	Read alignment 5' end includes forward primer​	● ​	● ​	​	​
	Read alignment 3' end includes reverse primer​	● ​	● ​	​	​
	Read alignment 5' end includes forward primer and 3' end includes reverse primer​	● ​	● ​	​	​
	Paired read including at least one primer in each has same leader–TRS junction in alignments​	● ​	● ​	​	​
	Read alignment 3' with >1 ployA​	​	● ​	● ​	​
	Read alignment 3' with >5 ployA​	​	● ​	● ​	​