CAGE peaks (hg38 v3)

CAGE peaks === This folder contains the CAGE peaks defined in the FANTOM5 project as a robust set, where genomic coordinates originally defined on hg19 are lifted to hg38 by liftOver tool. By following the update, their annotations are also updated - see “CAGE_peaks_annotation” directory in the parent directory. - Inquiries: [e-mail] - Update: 2015-09-18 initial release 2016-07-22 ver.2 release 2017-04-14 ver.3 release Data files --- - hg38_liftover_CAGE_peaks_phase1and2.bed.gz : all lifted-over CAGE peaks using UCSC Lift-over - hg38_fair_CAGE_peaks_phase1and2.bed : fairly remapped CAGE peaks. - hg38_problematic_CAGE_peaks_phase1and2.bed : problematic CAGE peaks that were filtered out by QC - hg38_new_CAGE_peaks_phase1and2.bed : newly identified CAGE peaks in hg38 DPI clustering - hg19_droppped_CAGE_peaks_phase1and2.bed : unmapped CAGE peaks (in hg19 coordination) Description of the columns in CAGE peaks coordinates files --- This is baed on BED9 format, where the thickStart and thickEnd position represent representative TSS positions. (https://genome.ucsc.edu/FAQ/FAQformat.html#format1) - chromosome - start of CAGE peak region - end of CAGE peak region - name (ID) of the CAGE peak - score - strand of the CAGE peak - start of the representative TSS position - end of the representative TSS position (Note: end is always start+1) - rgb string for color coding (plus or minus strand only)

CAGE峰（CAGE peaks）
本文件夹收录FANTOM5项目定义的稳健型CAGE峰数据集，其原始基于hg19参考基因组的基因组坐标已通过liftOver工具（liftOver）转换至hg38版本。伴随坐标系统升级，配套注释信息也已同步更新，详情请参阅上级目录中的「CAGE_peaks_annotation」文件夹。
- 咨询邮箱：[e-mail]
- 更新日志：2015年9月18日首次正式发布；2016年7月22日发布v2版本；2017年4月14日发布v3版本

数据文件
- hg38_liftover_CAGE_peaks_phase1and2.bed.gz：经UCSC Lift-over工具完成坐标转换的全部CAGE峰压缩文件
- hg38_fair_CAGE_peaks_phase1and2.bed：经合理重定位后的CAGE峰文件
- hg38_problematic_CAGE_peaks_phase1and2.bed：经质量控制（QC）流程过滤剔除的不合格CAGE峰文件
- hg38_new_CAGE_peaks_phase1and2.bed：基于hg38参考基因组通过DPI聚类新鉴定得到的CAGE峰文件
- hg19_droppped_CAGE_peaks_phase1and2.bed：未完成坐标转换的原始hg19版本CAGE峰文件

CAGE峰坐标文件列说明
本数据集基于BED9格式（BED9）构建，其中thickStart与thickEnd字段用于表征典型转录起始位点（Transcription Start Site, TSS）的位置，详细格式规范可参考：https://genome.ucsc.edu/FAQ/FAQformat.html#format1。各列含义依次为：
1. 染色体名称
2. CAGE峰区域的起始基因组坐标
3. CAGE峰区域的终止基因组坐标
4. CAGE峰的名称（唯一标识符ID）
5. 得分值
6. CAGE峰对应的DNA链方向
7. 典型转录起始位点的起始坐标
8. 典型转录起始位点的终止坐标（注：该字段值恒为起始坐标加1）
9. 用于颜色编码的RGB字符串（仅用于区分正链与负链）