Additional file 2. Fig. S1. Benchmarking and comparison of different tools using ATAC-seq data. A) Peak quantification performance using bedtools and BAMscale (1, 4 and 8 execution threads). B) Comparison of raw read counts between bedtools and BAMscale in six ATAC-seq samples. C) IGV screenshot of a peak overestimated by bedtools in all samples, where read pairs align to different chromosomes. Fig. S2. Colocalization of ATAC-seq peaks. Peaks with > threefold opening had increased colocalization with H3K4me3 and H3K9ac compared to peaks with weaker or no increase. Fig. S3. Changes in histone ChIP-seq signal between MV4-11 and MV4-11R cells. A) H3K27me3 signal decreased, B) H3K27ac signal increased, and C) H3K4me3 signal did not change in the MV4-11R cells compared to the MV4-11 cells. Fig. S4. Stranded and unstranded RNA-seq coverage tracks created with BAMscale. Fig. S5. Comparison of deposited END-seq and OK-seq data reprocessed with BAMscale.
