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BedTools使用简介  

2013-05-23 08:33:34|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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curl http://bedtools.googlecode.com/files/BEDTools.***<version>***.tar.gz > BEDTools.tar.gz
tar -zxvf BEDTools.tar.gz
cd BEDTools
make clean
make all
ls bin
cp /bin/* usr/local/bin/

The BEDTools [Browser Extensible Data (BED) ] utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools.

  1. Intersecting two BED files in search of overlapping features.
  2. Culling/refining/computing coverage for BAM alignments based on genome features.
  3. Merging overlapping features.
  4. Screening for paired-end (PE) overlaps between PE sequences and existing genomic features.
  5. Calculating the depth and breadth of sequence coverage across defined "windows" in a genome.
  6. Screening for overlaps between "split" alignments and genomic features.
  1. intersectBed -a reads.bed -b genes.bed  ########get overlap form two files

  2. intersectBed -a reads.bed -b genes.bed -v   #####get unique from one file

Citation

Please cite the following article if you use BEDTools in your research:

  • Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.

Also note that pybedtools, the Python extension of BEDTools, has been published in Bioinformatics. It extends upon much of the functionality in BEDTools and provides a very powerful and flexible Python interface for manipulating and comparing genomic features in BED/VCF/GFF/GTF/SAM/BAM format.

  • Dale RK, Pedersen BS, and Quinlan AR. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics (2011). doi:10.1093/bioinformatics/btr539
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