Additional file 1 of Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes

Additional file 1: Figure S1. FOXA1 (JASPAR MA0148.3) and STAT3 (JASPAR MA0144.2) occupancy in IMR90, U2OS, and GBS (JASPAR MA0113.2) in K562 datasets before and after deduplication, as reported by FIMO. Table S1. Total number of peaks/binding events reported by the tools in IMR90, K562 and U2OS datasets. Table S2. Total number of binding events discovered by each peak caller for IMR90, K562, U2OS, after filtering out the PCR duplicates. Table S3. Total GBS motif occupancy (GBS motif hits (p-value <1e-4) reported by FIMO). Table S4. Peak length statistics for GEM, Genetrack, MACE, MACS, and Peakzilla when run on GR ChIP-exo datasets for IMR90, K562 and U2OS cell types.

附加文件1：图S1。由FIMO软件报道的IMR90、U2OS细胞中叉头框蛋白A1（FOXA1，JASPAR MA0148.3）与信号转导与转录激活因子3（STAT3，JASPAR MA0144.2）的结合占据信号，以及K562数据集中GBS（JASPAR MA0113.2）的结合占据信号的去重前后结果。表S1：各工具在IMR90、K562及U2OS数据集上所报道的峰/结合事件总数。表S2：过滤掉PCR重复序列后，各峰调用工具在IMR90、K562及U2OS数据集上所发现的结合事件总数。表S3：GBS基序结合占据总况（即FIMO软件所报道的p值<1e-4的GBS基序匹配结果）。表S4：GEM、Genetrack、MACE、MACS及Peakzilla工具在IMR90、K562及U2OS细胞类型的GR ChIP-exo数据集上运行时所得到的峰长统计数据。