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CNVnator Install Instructions dmacmillan Bioinformatics 25 09-26-2016 02:59 AM
CNVnator: The format of cnv result zhk Bioinformatics 6 07-31-2014 10:52 AM
ROOT install + CNVnator issues milesgr General 2 01-01-2014 05:47 PM
what files are produced from CNVnator ? Kennels Bioinformatics 1 01-23-2012 09:14 AM
CNVnator for Non-human data BertieWooster Bioinformatics 0 06-07-2011 11:34 AM

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Old 04-28-2011, 07:17 AM   #1
menenuh
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Default couldn't run CNVnator

Hello,
Does anyone have experience with CNVnator?
It requires the ROOT package, and after two unsuccessful attempts I managed to install it finally. But now I'm having problems running it.
Am I the only one trying/failing?
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Old 05-10-2011, 05:00 PM   #2
southan
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Before you use cnvnator, you can go to (or not) "root/bin/" and type this line:
source thisroot.sh
It will automatically set your ROOTSYS.


Quote:
Originally Posted by menenuh View Post
Hello,
Does anyone have experience with CNVnator?
It requires the ROOT package, and after two unsuccessful attempts I managed to install it finally. But now I'm having problems running it.
Am I the only one trying/failing?
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Old 05-30-2011, 06:58 PM   #3
milesgr
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How did you get root to install? After like 15 minutes, I got the following:


/usr/bin/ld: /usr/local/lib/libfftw3.a(map-r2r-kind.o): relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libfftw3.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
gmake: *** [lib/libFFTW.so] Error 1


I downloaded the source...then did
export ROOTSYS=<path>/root

I then ran these commands from the root directory...
./configure
gmake

gmake resulted in the above error. Any thoughts?
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Old 05-30-2011, 07:53 PM   #4
milesgr
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Never mind, I figured it out. If anyone needs help, please feel free to post here.
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Old 06-11-2011, 01:55 PM   #5
CNVboy
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yeah, i have problem with the root package....how to change the path for the library? to edit the .bash_profile?
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Old 06-12-2011, 06:36 PM   #6
southan
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I use this line:
source /path/root/bin/thisroot.sh
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Old 06-13-2011, 07:05 AM   #7
CNVboy
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thx southan. I've been OK with both root and CNVnator compiling.
But now the question is, the command is like:
./cnvnator -root NA12878.root -chrom chr1 chr2 chr3 -tree NA12878_ali.bam

what's this NA12878.root? Is it some output of root package?

the documentation of CNVnator is really briefly-written and could be confusing to beginners like me.
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Old 06-13-2011, 08:45 AM   #8
ElMichael
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Quote:
Originally Posted by CNVboy View Post
thx southan. I've been OK with both root and CNVnator compiling.
But now the question is, the command is like:
./cnvnator -root NA12878.root -chrom chr1 chr2 chr3 -tree NA12878_ali.bam

what's this NA12878.root? Is it some output of root package?
It's just an output file that would be generated by the execution of the first CNVnator command (where extracted data from the input BAM file is written?) and, as far as I understand, would be used as a part of the input during the next CNVnator steps.
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Old 06-13-2011, 03:21 PM   #9
CNVboy
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thx Michael.

Now I've gone through the whole steps of CNVnator and seems quite good. The only problem now is at the final step about visualizing the CNV. I enter a genomic region at the prompt but got NO output shown as below:
./cnvnator -root NA18507.root -chrom chr1 -view 100
>chr1:246974801-247024800
>

It has already called CNV, but I just cannot visualize nor genotype.

btw, I'm wondering where is the output stored? Is it within some files?

thx
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Old 06-13-2011, 03:35 PM   #10
CNVboy
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Just now I tried the whole genome (no longer specific to chr1): ./cnvnator -root NA18507. root -tree ***.bam

Then it pop out:
Out of bound coordinate 199501844 for chromosome 'chr3'.
Out of bound coordinate 100338932 for chromosome 'chr15'.
Out of bound coordinate 100338932 for chromosome 'chr15'.
Out of bound coordinate 100338931 for chromosome 'chr15'.
Out of bound coordinate 100338932 for chromosome 'chr15'.
Out of bound coordinate 78774759 for chromosome 'chr17'.
Out of bound coordinate 199501844 for chromosome 'chr3'.

Then it goes well:
........
........
Filling and saving tree for 'chr5' ...
Done with the tree.
Filling and saving tree for 'chr6' ...
Done with the tree.
Filling and saving tree for 'chr7' ...
Done with the tree.
Filling and saving tree for 'chr8' ...
Done with the tree.
Filling and saving tree for 'chr9' ...
Done with the tree.
Filling and saving tree for 'chr10' ...
Done with the tree.
.........
.........
I don't know what does this 'out of bound coordinate" mean....Anyone has any idea? thx
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Old 06-13-2011, 07:38 PM   #11
southan
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Quote:
Originally Posted by CNVboy View Post
thx Michael.

Now I've gone through the whole steps of CNVnator and seems quite good. The only problem now is at the final step about visualizing the CNV. I enter a genomic region at the prompt but got NO output shown as below:
./cnvnator -root NA18507.root -chrom chr1 -view 100
>chr1:246974801-247024800
>

It has already called CNV, but I just cannot visualize nor genotype.

btw, I'm wondering where is the output stored? Is it within some files?

thx
cnvnator -root NA18507.root -view 100

That's Ok.
Are you using ssh? If so, you should use ssh -X.
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Old 06-13-2011, 08:54 PM   #12
CNVboy
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yeah, I'm using ssh.

I google ssh option, and -X seems to mean to enable X11 forwarding....But I'm still confused about how this has anything to do with my problem of visualizing/genotyping/storation....

thx
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Old 06-14-2011, 04:06 AM   #13
gprakhar
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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
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Old 06-14-2011, 06:38 AM   #14
CNVboy
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thx guys.

I tried using ssh -X, but still doesn't work.

[xug@pem610-006 src]$ ./cnvnator -root NA18507.root -view 100
>chr12 11396601 11436500
>

I can see nothing except the new prompt.
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Old 06-16-2011, 12:42 AM   #15
gprakhar
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Hello CNVboy,

Can you please give a list of all the commands you are using for running CNVnator from starting,
and some details about the input files?

Regards,
Prakhar Gaur
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Old 06-16-2011, 06:58 AM   #16
CNVboy
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Thx Prakhar,

Sorry for my delayed response. The problem of viewing has been solved. Yeah, you are right, use ssh -X and it works! thx~

I'm actually now trying larger-scale data on cluster, and would definitely ask for your kind help if come across new problems.

best regard
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Old 06-30-2011, 09:05 PM   #17
zhk
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Is there anyone know the format of cnv result? For example:
deletion chr10:6070441-6074520 4080 0.674906 0.00834134 72162.3
It is very easy to understand the first three column mean, but is there any can explain the rest of column mean?
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Old 07-01-2011, 12:41 AM   #18
gprakhar
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Dear zhk,

I had asked the same question to the author (Alex Abyzov), here is the reply.

Quote:
The output is as follows:
CNV_type, coordinates, size, normalized_RD, p-val1, p-val2.
p-val1 -- is from t-test
p-val2 -- is from probability of RD valued within the region to be in
the tails of gaussian distribution (kind a z-score).
Regards,
pg
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Old 07-01-2011, 01:08 AM   #19
zhk
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Thx gprakhar,

Is that mean the larger of p-val1 and p-val2, the more confidence of the result?

Do you find that the value of p-val2 will be very large or small sometimes? How to explain this situation?

example:
deletion chr10:6070441-6074520 4080 0.674906 0.00834134 72162.3

Quote:
Originally Posted by gprakhar View Post
Dear zhk,

I had asked the same question to the author (Alex Abyzov), here is the reply.



Regards,
pg
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Old 07-02-2011, 02:59 AM   #20
gprakhar
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Hello,

I am not sure, have used the tool on simulated data only.
You can ask the author and please do let me know what he says.

Regards,
pg
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