ChIP-sequencing fragment coverage

Raw sequencing reads from H3K27ac ChIP and input DNA from lymphoblastoid cells of three TET2 mutation carriers and two wild-type family members were quality and adapter trimmed with cutadapt version 1.16 in Trim Galore version 0.3.7 using default parameters. Trimmed reads were aligned to hs37d5 reference genome using Bowtie2 (version 2.1.0). Duplicate reads were removed with samtools rmdup (v1.7). Fragment coverage of paired-end reads was calculated from bam files with BEDtools genomecov (v2.26.0).

原始测序读数来自携带TET2突变的三个淋巴母细胞系细胞和两个野生型家族成员的H3K27ac ChIP及输入DNA，经cutadapt版本1.16在Trim Galore版本0.3.7中按默认参数进行质量和适配器剪切。剪切后的读数使用Bowtie2（版本2.1.0）与hs37d5参考基因组进行比对。通过samtools rmdup（v1.7）移除重复读数。通过BEDtools genomecov（v2.26.0）从bam文件中计算了配对端读数的片段覆盖度。