## Parameter file for Bowtie2 PE
## Values in <...> reference column titles in targets file
PairSet	Name	Value
modules	NA	bowtie2/2.2.5
software	NA	bowtie2
cores	-p	4
other	NA	-k 50 --non-deterministic
reference	-x	./data/tair10.fasta
infile1	-1	<FileName1>
infile1	path	NA
infile2	-2	<FileName2>
infile2	path	NA
outfile1	-S	<FileName1>
outfile1	path	./results/
outfile1	remove	NA
outfile1	append	.sam
outfile1	outextension	.bam




