BED格式文件

BED (Browser Extensible Data) format provides a flexible way to define the data lines that are displayed in an annotation track.

BED (Browser Extensible Data)格式文件就是通过规定行的内容来展示注释信息

BED文件每行至少包括chrom，chromStart，chromEnd三列；另外还可以添加额外的9列，这些列的顺序是固定的。

BED文件必须的3列:

1. chrom - 染色体号.
2. chromStart - feature在染色体上起始位置. The first base in a chromosome is numbered 0.
3. chromEnd - feature在染色体上末尾位置。染色体上前100个碱基位置标记为chromStart=0, chromEnd=100.The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.

BED文件可选的9列:

4. name - BED行名，在基因组浏览器左边显示；
5. score - 在基因组浏览器中显示的灰度设定，值介于0-1000；

gray score

6. strand - 正负链标记. Either "." (=no strand) or "+" or "-".

7. thickStart - feature起始位置(for example, the start codon in gene displays)。 When there is no thick part, thickStart and thickEnd are usually set to the chromStart position.

8. thickEnd - feature编码终止位置 (for example the stop codon in gene displays).

9. itemRgb - R,G,B (e.g. 255,0,0)值，当itemRgb 设置为 "On"，BED的行会显示颜色.

10. blockCount - blocks (exons)数目.

11. blockSizes - blocks (exons)大小列表，逗号分隔，对应于blockCount.

12. blockStarts -blocks (exons)起始位置列表，逗号分隔，对应于blockCount.；这个起始位置是与chromStart的一个相对位置。

Example: a complete BED definition

track name=pairedReads description="Clone Paired Reads" useScore=1
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601

The first three required BED fields are

1. chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
2. chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
3. chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.

The 9 additional optional BED fields are:

4. name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.

5. score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). This table shows the Genome Browser's translation of BED score values into shades of gray:
   

   gray score

6. strand* - Defines the strand. Either "." (=no strand) or "+" or "-".

7. thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays). When there is no thick part, thickStart and thickEnd are usually set to the chromStart position.

8. thickEnd - The ending position at which the feature is drawn thickly (for example the stop codon in gene displays).

9. itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.

10. blockCount - The number of blocks (exons) in the BED line.

11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.

12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount

参考：

• BED format