[jaycee]

hi CNV boy, can you let me know why ssh -X works on yours? It's not working on mine. Thanks!

[clarissaboschi]

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??

[clarissaboschi]

I have solved my problem, I do not need to include the name of the fasta file for each chromosome....it worked!

example

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?

[clarissaboschi]

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

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):

Can't determine length for 'chr1.fa'. No reference genome specified.

I tried different command lines, and always the same error

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?

[SD2010Bioinfo]

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

[bewlib]

I use ssh -X [email protected]…… ,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 ??

[bewlib]

CNVnator

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 ??

[jsbae]

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!!

[yeweijian]

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?

[aaronh]

Check out the supplemental in the CNVnator paper for a discussion on bin sizes and sensitivity.

http://www.ncbi.nlm.nih.gov/pubmed/21324876

[Robby]

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

[dmacmillan]

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...

[dmacmillan]

You have to "cd" into CNVnator/src/samtools and then "make", so libbam.a is created.

Also remember to type

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ROOTSYS}/lib

Then type

cd ..

to get back into your CNVnator/src directory and type

make

again

[djeffares]

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 :-)

[dmacmillan]

Try simply by typing this:

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!