[djeffares]

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

[gprakhar]

Regards,
--
pg

[elisadouzi]

Thanks! I got it.

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.

[CNVboy]

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.

[elisadouzi]

Hi milesgr,
I'm in the cluster and can not get into the root. How can I install the CNVnator?

Thanks!

Never mind, I figured it out. If anyone needs help, please feel free to post here.

[zhk]

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

[gprakhar]

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

[zhk]

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

Dear zhk,

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



Regards,
pg

[gprakhar]

Dear zhk,

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

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

[zhk]

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?

[CNVboy]

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

[gprakhar]

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

[CNVboy]

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.

[gprakhar]

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

[CNVboy]

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