BreakDancer的安装与使用

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所属分类:Genomics

安装BreakDancer总共需要完成以下三个软件的安装工作

  • Perl
  • Samtool
  • BreakDancer Software

安装perl语言 (一般linux系统已经自带了)以及相关的package

下载额外的GD Graphics Library ( Download from CPAN )

  • GD-1.18
  • GDGraph-1.44
  • GDGraph-histogram-1.1
  • GDTextUtil-0.86
  • Math-CDF-0.1
  • Statistics-Descriptive-3.0100

安装Library(以GD-1.18为例, 详细内容可参考每个Library的Readme文件)

tar -zvxf GD-1.18.tar.gz

cd GD-1.18

perl Makefile.PL

make

make install

Samtool的安装方法

在之前我已经在这个网站上面介绍了Samtool的安装方法,可以参考https://www.plob.org/2011/03/06/6.html

将Samtool加入PATH

编辑home目录底下的.profile文件

在export PATH之前加入PATH="${PATH}:samtool文件夹的绝对路径"

以samtool资料夹绝对路径为/home/bioinfo/samtool为例修改.profile檔案

在export PATH之前加入PATH="${PATH}:/home/bioinfo/samtool"

BreakDancer

下载BreakDancer (download from BreakDancer Source Forge:http://breakdancer.sourceforge.net/)

breakdancer-1.1_2011_02_21.zip

解压

unzip  breakdancer-1.1_2011_02_21.zip

安装BreakDancer

#进入breakdancer-1.1_2011_02_21/cpp文件夹

cd breakdancer-1.1_2011_02_21/cpp

#编译

make

使用流程

准备资料

Paired-end short read alignment data (*.bam)

检测流程(以现有的资料human.bam为例)

产生lst檔案

perl bam2cfg.pl human.bam > human.lst

检测Structural Variant

perl BreakDancerMax.pl human.lst > human.SV.output

检测Small InDel

perl BreakDancerMini.pl human.lst > human.InDel.output

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    • avatar boya888 3

      简介BreakDancer is an application for detecting structural rearrangements
      突变侦测 Insertion / Deletion / Inversion / Translocation
      核心技术 Poission Test / Fisher’s method / Kolmogorov-Smirnov test

      BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation.

        • avatar ybzhao Admin

          @boya888 boya888对BreakDancer 很了解啊,哈哈。这个是我们实验室的一个兄弟提供的信息。你如果了解更多希望与我们大家一起分享啊,O(∩_∩)O哈哈~

          • avatar flzh628 0

            @boya888 您好!有个问题想咨询。我在运行breakdancer的第一步时,老是报错,提示找不到Statistics-Descriptive,但是我装了这个模块啊,也添加到自己的环境变量中了。请问如何解决呢?谢谢您!下面是报错信息:“Can’t locate Statistics/Descriptive.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at bam2cfg.pl line 7.
            BEGIN failed–compilation aborted at bam2cfg.pl line 7.”