Quick Start

Stranded, paired-end, insert size = 200 bp:

$ rnnotator.pl -strP 200 sampleA.fq sampleB.fq

Non-stranded, paired-end, insert size = 200 bp:

$ rnnotator.pl -nonP 200 sampleA.fq sampleB.fq

Mixed library types:

$ rnnotator.pl –nonS sampleA.fq sampleB.fq –strP 150 sampleC.fq