Blahah/transrate — pull request #84 by MatthewRalston (2014-08-14 12:59:53+00:00)
Title: Stranded

This feature allows the strand specific alignment of reads to the transcriptome. By default, this feature include the 'unpaired' branch and it's statistical calculations. The user may specify one of 'fr' 'rf' 'ff' or 'f' strand specificity and supply paired and/or unpaired strand specific reads. Unpaired reads must have 'f' strand specificity for all strand specific options., this may be accomplished easily with your favorite fastq processing suite.