## Parameter file for HISAT2		
## Values in <...> reference column titles in targets file		
PairSet	Name	Value
modules	NA	hisat2/2.1.0
software	NA	hisat2
cores	-p	4
other	NA	-k 1 --min-intronlen 30 --max-intronlen 3000
outfile1	-S	<FileName1>
outfile1	path	./results/
outfile1	remove	NA
outfile1	append	.hisat.sam
outfile1	outextension	.hisat.bam
reference	NA	./data/tair10.fasta
infile1	-1	<FileName1>
infile1	path	NA
infile2	-2	<FileName2>
infile2	path	NA
