Uses how_are_we_stranded_here, a python package for testing strandedness. Runs Kallisto and Rseqc (infer-experiment-py) to to check which direction reads align once mapped in transcripts. It first creates a Kallisto index (or uses a pre-made index) of your organism's transcriptome. It then maps a small subset of reads (default 200000) to the transcriptome and uses Kallisto's --genomebam argument to project pseudoalignments to the genome sorted BAM file. (Currently only Kallisto version 0.44.0 works well with how_are_we_stranded_here.) It finally runs RSeQC's infer_experiment.py to check which direction reads from the first and second pairs are aligned in relation to the transcript strand, and provides output with the likely strandedness of your data.