CNVnator Inputs and Outputs
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Entering edit mode
4.6 years ago
styer.alex ▴ 10

Hi all,

I've just begun using CNVnator on some test files but am not quite sure what's going on with the output. Take the first couple steps as an example:

GENERATING A HISTOGRAM

$./cnvnator [-genome name] -root file.root [-chrom name1 ...] -his bin_size [-d dir] This step is not memory consuming and so can be done for all chromosomes at once. It can, of course, be carried for a subset of chromosomes also. Files with chromosome sequences are required and should reside in the running directory or in the directory specified by the -d option. Files should be named as: chr1.fa, chr2.fa, etc. CALCULATING STATISTICS$ ./cnvnator -root file.root [-chrom name1 ...] -stat bin_size

This step must be completed before proceeding to partitioning and CNV calling.

Both of these have run for me without error. It prints a few lines of standard output:

For GENERATING A HISTOGRAM:

Allocating memory ...

Done.

Calculating histograms with bin size of 1000 for 'Chr01' ...

Making GC histogram for 'Chr01' ...

Done.

Calculating histograms with bin size of 1000 for 'Chr02' ...

Making GC histogram for 'Chr02' ...

Done.

^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^

And for CALCULATING STATISTICS:

Making statistics for Chr01 ...

Making statistics for Chr02 ...

Average RD per bin (1-22) is 9.30194e-14 +- 56.7216 (before GC correction)

Average RD per bin (X,Y) is 0 +- 0 (before GC correction)

Correcting counts by GC-content for 'Chr01' ...

Correcting counts by GC-content for 'Chr02' ...

Making statistics for Chr01 after GC correction ...

Making statistics for Chr02 after GC correction ...

Average RD per bin (1-22) is 6.26884e-05 +- 4.66553e-06 (after GC correction)

Average RD per bin (X,Y) is 0 +- 0 (after GC correction)

HOWEVER, there are no other output files. For those who have used CNVnator before can you tell me if it's appending this information in some way to the original file.root file? Later steps do not require the std.out to be loaded in the command, but still require the original root file so I'm left with assuming it's being modified in some way.

Thanks!!

cnvnator cnv copy number variation genome • 3.0k views
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Entering edit mode
4.6 years ago

Hi! Assuming you didn't run into any errors, the data should be in the .root file created by the first command. You can view the file to confirm this by first running the root binary in terminal (/.../root-version/bin/root or just root if it's in your path) and then the following command in the root prompt:

new TBrowser()


This should open up a window that you can use to navigate to your .root file and view the generated histograms.