tophat输出结果junction.bed

BED format

 

BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required fields and nine additional optional fields. The number of fields per line must be consistent throughout any single set of data in an annotation track. The order of the optional fields is binding: lower-numbered fields must always be populated if higher-numbered fields are used.

If your data set is BED-like, but it is very large and you would like to keep it on your own server, you should use the data format.

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:
   shade
   score in range	≤ 166	167-277	278-388	389-499	500-611	612-722	723-833	834-944	≥ 945

6. strand - Defines the strand - either '+' or '-'.
7. thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays).
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.

Example:

Here's an example of an annotation track that uses a complete BED definition:

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

Example:

This example shows an annotation track that uses the itemRgb attribute to individually color each data line. In this track, the color scheme distinguishes between items named "Pos*" and those named "Neg*". See the usage note in the itemRgb description above for color palette restrictions. NOTE: The track and data lines in this example have been reformatted for documentation purposes. This can be pasted into the browser without editing.

browser position chr7:127471196-127495720browser hide alltrack name="ItemRGBDemo" description="Item RGB demonstration" visibility=2itemRgb="On"chr7    127471196  127472363  Pos1  0  +  127471196  127472363  255,0,0chr7    127472363  127473530  Pos2  0  +  127472363  127473530  255,0,0chr7    127473530  127474697  Pos3  0  +  127473530  127474697  255,0,0chr7    127474697  127475864  Pos4  0  +  127474697  127475864  255,0,0chr7    127475864  127477031  Neg1  0  -  127475864  127477031  0,0,255chr7    127477031  127478198  Neg2  0  -  127477031  127478198  0,0,255chr7    127478198  127479365  Neg3  0  -  127478198  127479365  0,0,255chr7    127479365  127480532  Pos5  0  +  127479365  127480532  255,0,0chr7    127480532  127481699  Neg4  0  -  127480532  127481699  0,0,255

Example:

It is also possible to color items by strand in a BED track using the colorByStrand attribute in the as shown below. For BED tracks, this attribute functions only for custom tracks with 6 to 8 fields (i.e. BED6 through BED8). NOTE: The track and data lines in this example have been reformatted for documentation purposes. This can be pasted into the browser without editing.

browser position chr7:127471196-127495720browser hide alltrack name="ColorByStrandDemo" description="Color by strand demonstration"visibility=2 colorByStrand="255,0,0 0,0,255"chr7    127471196  127472363  Pos1  0  +chr7    127472363  127473530  Pos2  0  +chr7    127473530  127474697  Pos3  0  +chr7    127474697  127475864  Pos4  0  +chr7    127475864  127477031  Neg1  0  -chr7    127477031  127478198  Neg2  0  -chr7    127478198  127479365  Neg3  0  -chr7    127479365  127480532  Pos5  0  +chr7    127480532  127481699  Neg4  0  -

 

tophat输出结果junction.bed中定义的junction就是中间是intron两边是exon的这种序列结构, JUNC00000001包含两个exon和中间的intron

cat junctions.bed

track name=junctions description="TopHat junctions"test_chromosome 177     400     JUNC00000001    61      +       177     400     255,0,0 2       73,50   0,173test_chromosome 350     550     JUNC00000002    45      +       350     550     255,0,0 2       50,50   0,150

 

exon1: 177-250(display), 177-249(actual)

intron: 250-350(display), 250-349(actual)

exon2: 350-400(display), 350-399(actual)

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

用bed_to_junc转换后得到.juncs其中只保留了junction中intron的部分

cat new_list.juncs

test_chromosome 249     350     +test_chromosome 399     500     +

 <chrom> <left> <right> <+/->

 

http://genome.ucsc.edu/FAQ/FAQformat.html#format1

http://www.ensembl.org/info/website/upload/bed.html

http://zhongguozhanying.blog.163.com/blog/static/21618709520135484450746/

http://blog.sina.com.cn/s/blog_7cffd14001012rtd.html

https://github.com/WormBase/wormbase-pipeline/blob/master/scripts/align_RNASeq.pl