Figure 3
Performance benchmark of different strategies. A. Pre-processing time for different alignment sizes: Coverage calculation time for Tabix and bigWig is shown as vertical bars; Coverage compression and indexing combined time for Tabix and bigWig is shown as red square and green triangle trend lines, respectively; RLE calculates and encodes the coverage and the time is shown as a purple X-shape trend line. For the vertical bars, the scale is on the right y-axis. For the trend lines, the scale is on the left y-axis. B. Peak memory usage during pre-processing for different alignment sizes: RLE is shown as vertical bars whose scale is on the right y-axis; bigWig is shown as a red square trend line whose scale is on the left y-axis. C. File and index sizes for different alignment sizes: Bam, RLE, Tabix, and bigWig are shown as colour columns whose scale is on the left y-axis; Bam and Tabix index sizes are shown as trend lines whose scale is on the right y-axis. Please note that RLE, Tabix, and bigWig coverage files are all converted from BAM files, which incur extra storage. D. Alignment extraction time for all TSS ± 5 Kb regions on the mouse genome for different chunk sizes based on 10 million short reads. E. Coverage calculation time for all TSS ± 5 Kb regions on the mouse genome for chunk size of 100 based on 10 million short reads. F. Alignment extraction and coverage calculation combined time and peak memory usage for Bam and RLE for different alignment sizes. The size of the bubbles denotes memory usage and the vertical location of the bubble centers denotes time. Test is based on all TSS ± 5 Kb regions in the mouse genome.