Can someone explain the output of BIC-seq?

[anibhax]

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!

[lethalfang]

I'm trying BIC-seq. Just managed to install the R package, and trying it out on some tumor-normal paired bam files, but got an error. I'm not an expert in R. Does anyone know what's wrong here?

# Just a couple of small chromosomes for testing:
> bicseq <- BICseq(sample = '/PATH/TO/Our_Tumor.bam', reference = '/PATH/TO/Our_Normal.bam', seqNames=c("chr21", "chr22") )

> seqs <- getBICseg(object=bicseq, bin=100, lambda=2, winSize=200, quant=0.95, mult=1)
Error in .C("sort_rms_binning", as.integer(sample), length(sample), as.integer(reference), :
"sort_rms_binning" not resolved from current namespace (BICseq)

Thanks in advance.