Reprocessed CAGE peaks generated by FANTOM5 (mm10 v3)_CAGE_peaks_expression

<pre>CAGE peaks === This directory contains the CAGE peaks defined in the FANTOM5 project as a robust set, where genomic coordinates originally defined on mm9 are lifted to mm10 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 --- - mm10_liftover_CAGE_peaks_phase1and2.bed.gz : all lifted-over CAGE peaks using UCSC Lift-over - mm10_fair_CAGE_peaks_phase1and2.bed : fairly remapped CAGE peaks. - mm10_problematic_CAGE_peaks_phase1and2.bed : problematic CAGE peaks that were filtered out by QC - mm10_new_CAGE_peaks_phase1and2.bed : newly identified CAGE peaks in mm10 DPI clustering - mm9_droppped_CAGE_peaks_phase1and2.bed : unmapped CAGE peaks (in mm9 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) </pre>

CAGE峰（CAGE peaks）
===
本目录包含FANTOM5项目定义的稳健CAGE峰集合，其原本基于mm9基因组版本定义的基因组坐标已通过liftOver工具转换为mm10版本。伴随坐标更新，相关注释信息也已同步更新——详情请参阅上级目录中的"CAGE_peaks_annotation"目录。

- 咨询邮箱：[e-mail]
- 更新日志：2015年9月18日 首次发布；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
- mm10_liftover_CAGE_peaks_phase1and2.bed.gz：通过UCSC Lift-over工具转换得到的全部CAGE峰文件
- mm10_fair_CAGE_peaks_phase1and2.bed：经标准化重映射的CAGE峰文件
- mm10_problematic_CAGE_peaks_phase1and2.bed：经质量控制（QC）过滤剔除的异常CAGE峰文件
- mm10_new_CAGE_peaks_phase1and2.bed：在mm10版本中通过DPI聚类（DPI clustering）新鉴定得到的CAGE峰文件
- mm9_droppped_CAGE_peaks_phase1and2.bed：未成功映射的mm9版本坐标CAGE峰文件

### CAGE峰坐标文件列说明
本文件基于BED9格式（BED9 format）构建，其中thickStart与thickEnd字段代表典型转录起始位点（TSS, Transcription Start Site）的位置（参考链接：https://genome.ucsc.edu/FAQ/FAQformat.html#format1）。各列含义如下：
1. 染色体
2. CAGE峰区域的起始坐标
3. CAGE峰区域的终止坐标
4. CAGE峰的名称（ID）
5. 分值
6. CAGE峰的链方向
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：终止坐标恒等于起始坐标+1）
9. 用于颜色编码的RGB字符串（仅适用于正链与负链）