tophat 原理_TopHat的使用以及输出文件

chrom(test_chromosome): The name of the chromosome.

这里就是test_chromosome

chromStart(177): The starting position of the feature in the

chromosome or scaffold. The first base in a chromosome is numbered

0.

chromosome上feature(在这里就是junction)的起始位置

chromEnd(400): 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.对应的终止位置

name(JUNC00000001): Defines the name of the BED line.

score(61): A score between 0 and 1000.

strand(+): Defines the strand: either '+' or '-'.

thickStart(177): The starting position at which the feature is

drawn thickly (for example, the start codon in gene displays).

thickEnd(400): The ending position at which the feature is

drawn thickly (for example, the stop codon in gene displays).

itemRgb(255,0,0): 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.

blockCount(2): The number of blocks (exons) in the BED line.

外显子个数，2个

blockSizes(73,50): A comma-separated list of the block sizes.

The number of items in this list should correspond to

blockCount.外显子大小，两个数字用逗号隔开

blockStarts(0,173): 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.

外显子起始位置，不从chromosome的起始开始，而是从chromStart开始数，也就是junction的起始位置开始计算，第一个碱基是0