Question: Problem using Breakdancer
0
gravatar for jamessemaj712
18 months ago by
jamessemaj71210 wrote:

Hi,

I am trying to use BreakDancer tool for detecting structural variants.I downloaded BreakDancer from http://gmt.genome.wustl.edu/packages/breakdancer/install.html

I did the installation steps mentioned on the page completely.After this I went to the Documentation section to read about running BreakDancer.It said to use the command /usr/lib/breakdancer-max/bam2cfg.pl -g -h NA19238_chr21_del_inv.bam NA19238_chr21_del_inv.bam > BRC6.cfg. But it gave an error saying:/usr/lib/breakdancer-max/bam2cfg.pl So I searched and there was no Breakdancer installed there.So I went to the folder where I had installed it and tried searching bam2cfg.pl but count not find it unless I finally found it in perl folder.Then I tried running the following command: sudo ./bam2cfg.pl -g -h NA19238_chr21_del_inv.bam NA19238_chr21_del_inv.bam > BRC6.cfg

I got error: Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.20.2 /usr/local/share/perl/5.20.2 /usr/lib/x86_64-linux-gnu/perl5/5.20 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.20 /usr/share/perl/5.20 /usr/local/lib/site_perl .) at ./bam2cfg.pl line 7. BEGIN failed--compilation aborted at ./bam2cfg.pl line 7.

Whats wrong please help

breakdancer • 703 views
ADD COMMENTlink modified 11 weeks ago by Biostar ♦♦ 20 • written 18 months ago by jamessemaj71210
0
gravatar for mastal511
18 months ago by
mastal5111.7k
mastal5111.7k wrote:

It looks like you have the Perl version of Breakdancer, which requires the Perl module mentioned in the error message.

Here is a link to the page with the instructions for the Perl version of Breakdancer:

http://breakdancer.sourceforge.net/moreperl.html

ADD COMMENTlink written 18 months ago by mastal5111.7k

I dont know how to use perl.I want to use c++ version,but where to get it explicitly without requiring to interfere with perl.I mean can you provide me the link explicitly for c++ version and explanation to running it.

ADD REPLYlink written 18 months ago by jamessemaj71210
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