This folder contains 63 files for the counts of various alignments in each simulation and mapping tests. The data are explained as follows. Each file name indicates the simulation parameters. For example, the file _ACTB_10000_5.35_1.100.counts was derived from the following simulation run: ACTB gene, 10000 reads, segment length range [5,35] and gap length range [1,100]. Together, the tests include 3 genes, 7 segment length ranges and 3 gap length ranges (3x9x3=63). 

The file contains 25 lines, for 5 mapping runs: 1. Bowtie2_Aligater, 2. Bowtie2_hyb, 3. STAR_default, 4. STAR_optimized first round, 5. STAR_optimized second round. Each run outputs counts for 5 types of alignments: 1. Primary alignments. 2. Correct alignments. 3. Suboptimal alignments. 4. correct Forward alignments. 5. correct Backward alignments. For the two rounds of STAR_optimized mappings, the correct alignments are added up as the final correct alignments. 
