Question: Can Someone Explain The Output Of Bic-Seq
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gravatar for Jordan
5.6 years ago by
Jordan1.1k
Pittsburgh
Jordan1.1k wrote:

Hi,

I'm using BIC-seq to identify CNVs in whole genome data. While I have been able to generate the output successfully, I'm having more trouble trying to understand the output. I could not find any information about the output in their home page. So I was hoping someone would break it down and explain it to me. It is my first time dealing CNV's, so I'm not really sure what to expect in the output either.

I gave the following command:

BIC-seq.pl --bin_size=30 --paired bic-seq.config Output BIC_CNVs

And it generated 4 kinds of files (.bicseg, .bic, .png, .wig)

This is a .bicseg file output generated by the tool.

chrom    start    end    caseRead    controlRead    log2.copyRatio    log10.pvalue
chr1    9991    564570    3012    3242    -0.0658    0
chr1    564571    567360    2324    368    2.6992    -312.8653
chr1    567361    568650    11219    312    5.2086    -2300.0146
chr1    568651    569610    748    117    2.7169    -95.7837

In the .bicseg file, I would like to know what caseRead and controlRead mean? I don't understand that part at all. And also all the start and end seem to follow a window. I thought the output would be more like these are the positions where CNV's are found or something like that. I mean CNVs can come in all sizes. They don't necessarily have to be uniform correct?

The output of a .bic file is like this,

2825201    5784298    0.488426    9991    9456600
135    142    0.950704    9456601    9456630
1383418    2865712    0.482748    9456631    13772280
2294577    4700197    0.488187    13772281    21341100

This is the output in a .wig file,

track type=wiggle_0 name="Bed Format" description="611_BIC_CNVs_Run3" visibility=dense color=200,100,0 altColor=0,100,200 priority=20
chr1 9991 564570 -0.0658
chr1 564571 567360 2.6992
chr1 567361 568650 5.2086
chr1 568651 569610 2.7169

From what I know of wig files, they don't look like this. It looks more like a bed file, except the header file. It does not even load in IGV browser. Any thoughts on that?

Thanks for the help!

cnv output • 2.5k views
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