bigBed及bigWig格式

-----------------------------bigBed---------------------------------

1、bigBed格式

BigBed文件是使用bedToBigBed程序從BED類型文件創建的。結果得到的bigBed文件是二進制索引文件。bigBed文件的主要優點是，僅將顯示特定區域所需的文件部分傳輸到Genome瀏覽器服務器。因此，在處理大數據集時，bigBed的顯示性能要比常規BED快得多。bigBed文件保留在本地web可訪問的服務器(http、https或ftp)上，而不在UCSC服務器上，並且只有當前顯示的染色體位置所需的部分被本地緩存為“稀疏文件”

2、創建

2.1、從bed文件創建

bed文件必須先以chrom 排序，在以chromStart排序

sort -k1,1 -k2,2n unsorted.bed > input.bed   #bed文件必須先排序

2.2、移除bed文件中 "track" or "browser" lines

2.3、利用fetchChromSizes工具生成chrom.sizes文件

2.4、利用bedToBigBed生成BigBed文件

bedToBigBed input.bed chrom.sizes myBigBed.bb

 2.5、拖到瀏覽器中

 2.6、其它工具

bigBedToBed — converts a bigBed file to ASCII BED format.
bigBedSummary — extracts summary information from a bigBed file.
bigBedInfo — prints out information about a bigBed file.

 ---------------------------------bigwig---------------------------------

1、bigwig格式

bigWig格式對於密集、連續的數據非常有用，這些數據將在基因組瀏覽器中顯示為圖形。BigWig文件是使用wigToBigWig程序從wiggle (wig)類型文件創建的。bigWig文件是索引的二進制格式。這種格式的主要優點是，只將文件中顯示特定區域所需的部分傳輸到Genome瀏覽器服務器。在處理大型數據集時，bigWig文件的顯示性能要比常規的wiggle文件快得多。Wiggle數據必須是連續的，並且由大小相等的元素組成。如果您的數據是稀疏的或包含不同大小的元素，請使用bedGraph格式而不是wiggle格式。如果您有一個非常大的bedGraph數據集，您可以使用bedGraphToBigWig程序將其轉換為bigWig格式。

Step 1. Create a wig format file following the directions here. When converting a wig file to a bigWig file, you are limited to one track of data in your input file; therefore, you must create a separate wig file for each data track.

Step 2. Remove any existing "track" or "browser" lines from your wig file so that it contains only data.

Step 3. Download the wigToBigWig program from the binary utilities directory.

Step 4. Use the fetchChromSizes script from the same directory to create the chrom.sizes file for the UCSC database with which you are working (e.g., hg19). If the assembly genNom is hosted by UCSC, chrom.sizes can be a URL like: http://hgdownload.soe.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes

Step 5. Use the wigToBigWig utility to create the bigWig file from your wig file:

wigToBigWig input.wig chrom.sizes myBigWig.bw

Note that the wigToBigWig program also accepts gzipped wig input files.

Step 6. Move the newly created bigWig file (myBigWig.bw) to a web-accessible http, https, or ftp location.

Step 7. If the file name ends with a .bigWig or .bw suffix, you can paste the URL directly into the custom track management page, click "submit" and view the file as a track in the Genome Browser. By default, the file name will be used to name the track. To configure the track label or other visualization options, you must create a track line, as shown in Step 8.

Step 8. Construct a custom track using a single track line. The most basic version of the track line will look something like this:

track type=bigWig name="My Big Wig" description="A Graph of Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigWig.bw

Paste the custom track line into the text box on the custom track management page.

The wigToBigWig program can be run with several optional parameters, including:

 

http://genome.ucsc.edu/goldenPath/help/bigBed.html
http://genome.ucsc.edu/goldenPath/help/bigWig.html