Allo-only and UMR peak calls for 481 K562 datasets

We analyzed the ENCODE public database, focusing specifically on ChIP-seq experiments in K562 cells. From 774 qualifying experiments (retrieval date Feb. 2023), we selected 481 based on the criteria that the dataset had at least one replicate, had a control file, no major audits from ENCODE, and resulted in non-zero peak calls in the UMR sample using our pipeline. We also only analyzed one dataset per transcription factor, which was randomly selected from the selection of those available. We retrieved FASTQ files for both single- and paired-end experiments. Replicates were concatenated and aligned using Bowtie 2 v.2.5.1, reporting 25 valid alignments per read with parameters “--no-mixed --no-discordant” for paired-end reads. The alignments were sorted using SAMamtools v1.16.1 collate. We employed Allo on the sorted alignments to obtain rescued reads. For control experiments, reads were randomly assigned during Allo processing (--random). Following alignment and rescue, peaks were subsequently identified using MACS2 v2.7.1, with the argument “-f BAMPE” for paired-end experiments. ENCODE blacklist regions were excluded using BedtoolsBEDTools v2.27.1 intersect -v.本研究针对ENCODE公共数据库展开分析，重点聚焦K562细胞中的染色质免疫共沉淀测序（ChIP-seq）实验。研究从检索日期为2023年2月的774个合格实验中，依据以下标准筛选出481个数据集：该数据集至少包含1个生物学重复、配有对照文件、未收到ENCODE的重大审核意见，且通过本研究的分析流程在UMR样本中获得了非零的峰调用结果。此外，本研究仅为每个转录因子选取一个数据集，从可用数据集中随机抽取。我们检索了单端与双端测序实验对应的FASTQ文件。将生物学重复的数据合并后，使用Bowtie 2 v.2.5.1进行序列比对：针对双端测序数据，设置参数"--no-mixed --no-discordant"，每条读段最多报告25个有效比对结果。随后使用SAMtools v1.16.1的collate子命令对排序后的比对结果进行整理。我们采用Allo工具处理排序后的比对文件，以提取救援读段。对于对照实验，在Allo处理过程中通过参数"--random"对读段进行随机分配。完成比对与读段救援后，使用MACS2 v2.7.1开展峰调用分析：针对双端测序数据，设置参数"-f BAMPE"。最后通过BEDTools v2.27.1的intersect -v命令，排除ENCODE黑名单区域的序列。