UCSC常见格式：http://genome.ucsc.edu/FAQ/FAQformat.html UCSC工具：http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

1 Wig

http://genome.ucsc.edu/goldenPath/help/wiggle.html

示例：

  1. fixedStep chrom=chr3 start=400601 step=100
  2. 11
  3. 22
  4. 33

2 bigWig

http://genome.ucsc.edu/goldenPath/help/bigWig.html wig生成的带索引的二进制文件，eg. bigWigExample.bw eg. hg19.chrom.sizes

生成命令：

  1. wigToBigWig input.wig chrom.sizes myBigWig.bw

查看命令：

  1. bigWigToBedGraph
  2. bigWigToWig
  3. bigWigSummary
  4. bigWigAverageOverBed
  5. bigWigInfo

3 bedGraph

http://genome.ucsc.edu/goldenPath/help/bedgraph.html 提取bigWig文件

  1. bigWigToBedGraph byBigWig.bw out.bedGraph

示例：

  1. browser position chr19:49302001-49304701
  2. browser hide all
  3. browser pack refGene encodeRegions
  4. browser full altGraph
  5. #    300 base wide bar graph, autoScale is on by default == graphing
  6. #    limits will dynamically change to always show full range of data
  7. #    in viewing window, priority = 20 positions this as the second graph
  8. #    Note, zero-relative, half-open coordinate system in use for bedGraph format
  9. track type=bedGraph name="BedGraph Format" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20
  10. chr19 49302000 49302300 -1.0
  11. chr19 49302300 49302600 -0.75
  12. chr19 49302600 49302900 -0.50
  13. chr19 49302900 49303200 -0.25
  14. chr19 49303200 49303500 0.0
  15. chr19 49303500 49303800 0.25
  16. chr19 49303800 49304100 0.50
  17. chr19 49304100 49304400 0.75
  18. chr19 49304400 49304700 1.00