CNV-seq, to detect Copy Number Variation using next-generation sequencing

[xiechao]

CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

more details at BMC Bioinformatics :
http://www.biomedcentral.com/1471-2105/10/80

The package is at
http://tiger.dbs.nus.edu.sg/cnv-seq

[zlu]

This may be really obvious but I'm trying to understand how to you decide which is ref and which is test. If I have 2 bam files generated by mapping Illumina reads from 2 individuals against the NCBI reference genome, does it mean either one can be ref or test?

[adamreid]

Hi,

I want to check my genome sequence for collapsed, tandemly repeated genes. It seems to me that I could use software for detecting CNVs in that I am looking for significantly increased read depth. CNV-seq requires test and reference sequences, which makes sense to control for sequence-based noise in read depth however I only have my reference genome and one instance of Illumina data. Does anyone have any ideas?

Adam

[roman.sergio]

Hi,

I am trying to undertand how to build the file for CNV detection with sequence.
I would like to know wich information is need it on the files.

Do you have some examples?

[louis7781x]

Originally Posted by xiechao

CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

more details at BMC Bioinformatics :
http://www.biomedcentral.com/1471-2105/10/80

The package is at
http://tiger.dbs.nus.edu.sg/cnv-seq

Hi,I want to know:CNV-seq input file is DNA-seq or RNA-seq?

[roman.sergio]

Hi !

My data are DNA-seq. But there are not from one Case-control study.

I working on the human Chr 8. I use a reference sequence to simulate my DNA-seq. I just would like to know if some parameters that I modify on my simulation influence the CNV detection on my DNA-seq.

Some ideas?

Sergio

[roman.sergio]

Hello

Did you already found how to detect the CNV with your data from non control case study?

I am continuing seraching for a solution.

Regards,

Sergio

[jflores]

Originally Posted by louis7781x

Hi,I want to know:CNV-seq input file is DNA-seq or RNA-seq?

Hi Louis,

CNV-seq input consists in just two files (reference & test) with just two columns each.
First column corresponds to the third column in a BAM file, that is the reference sequence name of the alignment (Chr1, Chr2, ..), the second column is the fourth column of a BAM file, that is the corresponding 1-based leftmost mapping position of that read. Input files can look like this:

1 999
1 1234
1 23456
1 25234

Full explanation of the input, how to get it, how to run CNV-seq, etc:

http://tiger.dbs.nus.edu.sg/cnv-seq/doc/manual.pdf


Jose Flores

[jflores]

Originally Posted by roman.sergio

Hello

Did you already found how to detect the CNV with your data from non control case study?

I am continuing seraching for a solution.

Regards,

Sergio

Hi Sergio,

With CNV-seq in mind and for non-control-case studies you can basically choose whatever reference you want. There might be some issues to worry about like what population the reference you choose come from? or what's the coverage .. It will depend on your purpose and the features of your sample to analyze.
I’ve seen some studies taking the health individual NA10851 from the 1000 genomes data as a control/reference.

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/

Hope can help,
Jose Flores

[louis7781x]

Originally Posted by jflores

Hi Louis,

CNV-seq input consists in just two files (reference & test) with just two columns each.
First column corresponds to the third column in a BAM file, that is the reference sequence name of the alignment (Chr1, Chr2, ..), the second column is the fourth column of a BAM file, that is the corresponding 1-based leftmost mapping position of that read. Input files can look like this:

1 999
1 1234
1 23456
1 25234

Full explanation of the input, how to get it, how to run CNV-seq, etc:

http://tiger.dbs.nus.edu.sg/cnv-seq/doc/manual.pdf


Jose Flores

Thanks for your help,I want to know the input type because the coverage of DNA-seq and RNA-seq is different.So if I use RNA-seq aligned to ref genome and use output file bam to run CNV-seq,Does it apply to analyze copy number varivation?

[tonio100680]

Hi,

how to view the level of a gene in CNV-seq ?

Script :
samtools view Patient_test/Parsed_X/chr17.fa/bam/sorted.bam | perl -lane 'print "$F[2]\t$F[3]"' > test.hits
samtools view Patient_ref/Parsed_X/chr17.fa/bam/sorted.bam | perl -lane 'print "$F[2]\t$F[3]"' > ref.hits

perl cnv-seq.pl --test test.hits --ref ref.hits --genome chrom17

data <- read.delim("test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.minw-4.cnv")
cnv.print(data)
cnv.summary(data)
plot.cnv(data)
ggsave("sample.pdf")
[IMG]/home/labo/Sample1.pdf[/IMG]

Regards

[jflores]

Hi Tonio,

You can plot specific coordinates and try to infer from that if your gene of interest has or not gain/loss of copies.

Script :
samtools view Patient_test/Parsed_X/chr17.fa/bam/sorted.bam | perl -lane 'print "$F[2]\t$F[3]"' > test.hits
samtools view Patient_ref/Parsed_X/chr17.fa/bam/sorted.bam | perl -lane 'print "$F[2]\t$F[3]"' > ref.hits

perl cnv-seq.pl --test test.hits --ref ref.hits --genome chrom17

data <- read.delim("test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.minw-4.cnv"))
plot.cnv.chr(data, chromosome=NA, from=NA, to=NA)

... For more options about plotting using CNV-seq you can have a look at the cnv.R file

Regards,

Rodrigo

[mimi_lupton]

Dear all,
I have a couple of questions regarding CNV-seq.
I am having a play around with some DNA sequencing that is from custom capture. I have analysed some BAM files using the program. Some work fine, but some file combinations come up with an error, which is strange as all the data has been produced and analysed in exactly the same way. The error is;

"Can't use an undefined value as an ARRAY reference at /share/apps/cnv-seq_1.0/bin/cnv-seq.pl line 204, <REF> line 6460211."

I think this is some kind of Perl script error??

Also does anyone have any experience of using capture data with CNV-seq? any advice would be greatly appreciated.

Thanks for you help

[gprakhar]

Dear xiechao,

I am trying to use CNV-seq for 36 length Read size simulated data. I am not detecting any CNV.
While for the same data with 76bp Read Length, CNV-seq detects CNV.

Is the read length hard coded in the script?

Is there a way to use CNV-seq on 36 length read data.

Thanking you,
pg

[DineshCyanam]

Originally Posted by louis7781x

Thanks for your help,I want to know the input type because the coverage of DNA-seq and RNA-seq is different.So if I use RNA-seq aligned to ref genome and use output file bam to run CNV-seq,Does it apply to analyze copy number varivation?

I have the same question too. It would be really great if someone can shed some light on it.

[gprakhar]

Originally Posted by cdinz

I have the same question too. It would be really great if someone can shed some light on it.

The input type will not vary, it will still be a BAM file aligned to the ref genome.
The difference comes in the analysis part.
You will have to take into consideration the Intron-Exon Junctions. As a Intron will be taken as a CNV. Also another problem is that if a CNV breakpiomt lies in the Intron, you can not come to know about it.
We have tumor Exome data, done by the True-Seq protocol, hence while doing the analysis use the co-ordinates provided by them.

[aggp11]

Originally Posted by mimi_lupton

Dear all,
I have a couple of questions regarding CNV-seq.
I am having a play around with some DNA sequencing that is from custom capture. I have analysed some BAM files using the program. Some work fine, but some file combinations come up with an error, which is strange as all the data has been produced and analysed in exactly the same way. The error is;

"Can't use an undefined value as an ARRAY reference at /share/apps/cnv-seq_1.0/bin/cnv-seq.pl line 204, <REF> line 6460211."

I think this is some kind of Perl script error??

Also does anyone have any experience of using capture data with CNV-seq? any advice would be greatly appreciated.

Thanks for you help

Hello mimi,

I am trying to work on custom capture data usin cnv-seq. Could you enlighten me on how it worked for you and any suggestions on how to use it would be greatly appreciated.

Thanks,
Praful

[pd]

Hello

I am analyzing CNVs for the first time or rather new to CNV-seq. Manual is pretty clear but i have one very basic doubt. I have my .bam file for which i can generate my.hits file as well using samtools. BUT from where do i get this ref.hits file. I have only one .bam file thats it which i would be using for my.hits file.. Some guidance?

[DineshCyanam]

Originally Posted by parveendabas

Hello

I am analyzing CNVs for the first time or rather new to CNV-seq. Manual is pretty clear but i have one very basic doubt. I have my .bam file for which i can generate my.hits file as well using samtools. BUT from where do i get this ref.hits file. I have only one .bam file thats it which i would be using for my.hits file.. Some guidance?

Hi Parveen,
The ref.hits would be from a normal/control sample... or if you don't have one... You can get the normal bam file from the 1000 Genomes project.

-Dinesh

[pd]

Thank you dinesh. But my data is not normal/control type and neither its related to 1000 genome project. Its one sample data. What should i do??