bigBed及bigWig格式

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

1、bigBed格式

BigBed文件是使用bedToBigBed程序从BED类型文件创建的。结果得到的bigBed文件是二进制索引文件。bigBed文件的主要优点是，仅将显示特定区域所需的文件部分传输到Genome浏览器服务器。因此，在处理大数据集时，bigBed的显示性能要比常规BED快得多。bigBed文件保留在本地web可访问的服务器(http、https或ftp)上，而不在UCSC服务器上，并且只有当前显示的染色体位置所需的部分被本地缓存为“稀疏文件”

2、创建

2.1、从bed文件创建

bed文件必须先以chrom 排序，在以chromStart排序

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

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、拖到浏览器中

 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格式对于密集、连续的数据非常有用，这些数据将在基因组浏览器中显示为图形。BigWig文件是使用wigToBigWig程序从wiggle (wig)类型文件创建的。bigWig文件是索引的二进制格式。这种格式的主要优点是，只将文件中显示特定区域所需的部分传输到Genome浏览器服务器。在处理大型数据集时，bigWig文件的显示性能要比常规的wiggle文件快得多。Wiggle数据必须是连续的，并且由大小相等的元素组成。如果您的数据是稀疏的或包含不同大小的元素，请使用bedGraph格式而不是wiggle格式。如果您有一个非常大的bedGraph数据集，您可以使用bedGraphToBigWig程序将其转换为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