tophat生成文件之BED文件格式

 BED 文件格式提供了一种灵活的方式来定义的数据行，以用来描述注释的信息。BED行有3个必须的列和9个额外可选的列。 每行的数据格式要求一致。

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).
染色体或scafflold 的名字(eg chr3， chrY, chr2_random, scaffold0671 )
2.chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
chromStart 染色体或scaffold的起始位置，染色体第一个碱基的位置是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.

chromEn 染色体或scaffold的结束位置，染色体的末端位置没有包含到显示信息里面。例如，首先得100个碱基的染色体定义为chromStart =0 . chromEnd=100, 碱基的数目是0-99

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.
指定BED行的名字，这个名字标签会展示在基因组浏览器中的bed行的左侧。
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:

 score 0到1000的分值，如果在注释数据的设定中将原始基线设置为１，那么这个分值会决定现示灰度水平（数字越大，灰度越高），下面的这个表格显示Genome Browser

6.strand - Defines the strand - either '+' or '-'.定义链的方向，''+” 或者”-” 　
7.thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays).thickStart 起始位置（The starting position at which the feature is drawn thickly）(例如，基因起始编码位置）
8.thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
终止位置（The ending position at which the feature is drawn thickly）（例如：基因终止编码位置）

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.
itemRGB 是一个RGB值的形式, R, G, B (eg. 255, 0, 0), 如果itemRgb设置为'On”, 这个RBG值将决定数据的显示的颜色。
10.blockCount - The number of blocks (exons) in the BED line.
blockCount BED行中的block数目，也就是外显子数目

11.blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
blockSize 用逗号分割的外显子的大小, 这个item的数目对应于BlockCount的数目

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.

 blockStarts- 用逗号分割的列表, 所有外显子的起始位置，数目也与blockCount数目对应.