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CNVnator Install Instructions dmacmillan Bioinformatics 25 09-26-2016 01:59 AM
CNVnator: The format of cnv result zhk Bioinformatics 6 07-31-2014 09:52 AM
ROOT install + CNVnator issues milesgr General 2 01-01-2014 04:47 PM
what files are produced from CNVnator ? Kennels Bioinformatics 1 01-23-2012 08:14 AM
CNVnator for Non-human data BertieWooster Bioinformatics 0 06-07-2011 10:34 AM

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Old 07-06-2011, 05:45 PM   #21
zhk
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Hello pg,
This is the replay from the author.

Those p-values are not very discriminate. The major cause of false
positives is read mismapping and sequencing biases.
Large events are generally more trustful
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Old 10-20-2011, 09:17 PM   #22
elisadouzi
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Hi milesgr,
I'm in the cluster and can not get into the root. How can I install the CNVnator?

Thanks!

Quote:
Originally Posted by milesgr View Post
Never mind, I figured it out. If anyone needs help, please feel free to post here.
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Old 10-21-2011, 06:07 AM   #23
CNVboy
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Quote:
Originally Posted by elisadouzi View Post
Hi milesgr,
I'm in the cluster and can not get into the root. How can I install the CNVnator?

Thanks!
What do you mean by "cannot get into root". Have you downloaded ROOT package?
You'd better download the newest version of ROOT.(Old version may have bugs)
Then install CNVnator.

btw, ROOT is large package, you may take some patience.
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Old 10-21-2011, 09:20 AM   #24
elisadouzi
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Thanks! I got it.

Quote:
Originally Posted by CNVboy View Post
What do you mean by "cannot get into root". Have you downloaded ROOT package?
You'd better download the newest version of ROOT.(Old version may have bugs)
Then install CNVnator.

btw, ROOT is large package, you may take some patience.
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Old 11-02-2011, 03:37 AM   #25
gprakhar
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Regards,
--
pg
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Old 01-05-2012, 12:20 AM   #26
djeffares
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Default Problems making CNVnator

Hi all,

I've got root installed, but now I'm having problems compiling CNVnator. When I type make, I get this error:

g++ -pthread -m64 -I/usr/local/root/bin/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
cc1plus: error: /usr/local/root/bin/root/include: Not a directory
make: *** [obj/cnvnator.o] Error 1

Any help much apreciated.
Dan
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Old 01-06-2012, 01:43 PM   #27
dmacmillan
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Try simply by typing this:

Code:
export ROOTSYS=[path to root installed directory]
replacing everything inside and including the square brackets by whatever directory you installed root to - e.g. /home/djaffares/root
then type 'make' and hit enter and it should work! Good luck Dan!

Last edited by dmacmillan; 01-06-2012 at 01:45 PM.
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Old 01-10-2012, 06:11 AM   #28
djeffares
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Default CNVnator, still not compiling

Thanks for this, but still no luck. here is what I did:
which root
/usr/local/bin/root

export ROOTSYS=/usr/local/bin/root
cd software/CNVnator/src/
make

#And I still get this error.

g++ -pthread -m64 -I/usr/local/bin/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
cc1plus: error: /usr/local/bin/root/include: Not a directory
make: *** [obj/cnvnator.o] Error 1

#thanks in advance for any ideas :-)
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Old 01-10-2012, 07:54 AM   #29
dmacmillan
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You have to "cd" into CNVnator/src/samtools and then "make", so libbam.a is created.

Also remember to type

Code:
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ROOTSYS}/lib
Then type
Code:
cd ..
to get back into your CNVnator/src directory and type
Code:
make
again
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Old 01-18-2012, 08:53 AM   #30
dmacmillan
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Also does anyone know what bin_size refers to? There is a bin size as in the .BAM bin size, but there is also the genomic bin size...
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Old 01-20-2012, 02:09 AM   #31
Robby
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Hello,

I am interested in the bin_size as well. Which bin_size do you use in the second step:

./cnvnator -root file.root -chrom ch1 -his bin_size

And is the bin_size the same for the following steps?

Thanks
Robby
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Old 01-23-2012, 03:10 PM   #32
aaronh
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Check out the supplemental in the CNVnator paper for a discussion on bin sizes and sensitivity.
http://www.ncbi.nlm.nih.gov/pubmed/21324876
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Old 04-11-2012, 11:44 PM   #33
yeweijian
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Now i have already called CNV,but i don't know the format of CNV result.
It does't look like "CNV_type coordinates CNV_size normalized_RD p-val1 p-val2"

It likes "deletion chr1:1-10000 10000 0 1.59373e-11 0 1.99216e-11 5.41313e-300 -1"

Why are my results a few more elements(columns)? And how to explain this situation?
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Old 07-18-2012, 07:04 AM   #34
jsbae
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Hello,

I have two qestions to show output.root and -genotype command.
1. After I sucessfully got a result by -call 100, I run -genotype. But I didn't show any result as following:
(command -call) ./cnvnator -root my_output.root -chrom chr20 -call 100
... displayed calls result...
(command -genotype) ./cnvnator -root my_output.root -chrom chr20 -genotype 100
> (no result)

Anyone know the reason? -view command also didn't give me any result.

2. In my output.root, I wish to know copy number as 0x, 1x. How can I show it, please?

Thanks your kind reply!!
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Old 12-23-2012, 09:41 PM   #35
bewlib
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Default CNVnator

Quote:
Originally Posted by gprakhar View Post
Hello CNVboy,

If you want to view anything other than text while using ssh, you will have to use the "-X" option.

Regards,
Prakhar Gaur

Would you give me a detail description about hou to use ssh -X to view genotype ??
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Old 12-23-2012, 10:40 PM   #36
bewlib
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I use ssh -X chengsj@11.11.1 ,but I can't see anything when I use
[xug@pem610-006 src]$ ./cnvnator -root NA18507.root -view 100
>chr12 11396601 11436500

would you help me ??
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Old 03-06-2013, 06:33 PM   #37
SD2010Bioinfo
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hello CNVboy,

I'm using Putty to log on our cluster. Could you tell me how to use ssh -X to visualising or genotyping the CNVnator result? Thanks
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Old 07-23-2014, 06:50 AM   #38
clarissaboschi
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Dear members

I am running CNVnator tool for chicken, but I am having some problems with step 2. I read many forums and also the manual and I did not get any solution for it.

I ran the first step and it was ok. My command line was
Code:
cnvnator -root 1.root -genome /home/genomes/Ggallus.fa -tree /home/Sample_1/1sort.bam
But in the second step I got the error message when I ran only for 1 chromosome (this fasta file file is in my current directory):
Code:
Can't determine length for 'chr1.fa'. No reference genome specified.
I tried different command lines, and always the same error
Code:
cnvnator -root 1.root -genome /home/genomes/Ggallus.fa   -chrom  1 chr1.fa -his 100

cnvnator -root 1.root -genome d /home/genomes/Ggallus.fa  -chrom  1 chr1.fa -his 100

cnvnator -root 1.root -genome /home/genomes/Ggallus.fa  -chrom  chr1 chr1.fa -his 100

cnvnator -root 1.root -genome /home/genomes/Ggallus.fa  -chrom  chr1.fa -his 100

Do you have any suggestion for it?
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Old 07-29-2014, 09:48 AM   #39
clarissaboschi
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I have solved my problem, I do not need to include the name of the fasta file for each chromosome....it worked!

example
HTML Code:
cnvnator -root 1.root -genome /home/genomes/Ggallus.fa -chrom 1 -his 100
Other comment I got much more deletions than duplications, is it the expected?
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Old 07-29-2014, 11:48 AM   #40
clarissaboschi
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Default Bin size

I know that there is information about the bin sizes in the supplemental material from CNVnator paper, and they recommend to test different sizes, and also higher the coverage, smaller the bin size.

I tested 3 different bins: 100, 150 and 200, and I got very different number of CNVs.
My coverage is about: 8-15X.

I dont know which bin is better to use...
Any suggestions??
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