geCNV

Options

Option	Description	Argument
--samples	Two sample names. The ratio is computed Sample2/Sample1 [required]	[char,char]
--gipOut	GIP output directory [default gipOut]	[char]
--outName	Output name [default gipOut/sampleComparison/geCNV]	[char]
--chrs	Chromosomes to use. If “NA” it uses the same chromsomes as GIP [default NA]	[char …]
--MAPQ	Label genes with MAPQ < –MAPQ [default 0]	[int]
--highLowRatio	Provide 2 numbers. Genes with ratio scores > num1 or < num2 will be colored differently [default 1.5 0.5]	[double,double]
--pseudocount	Normalized mean coverage pseudo count value preventing infinite (1/0) and NaN (0/0) ratio values [default 0.1]	[double]
--overview_ylim	Overview plot visualization threshold. Ratio values greather than this threshold are shown as –ylim [default 3]	[double]
--scaleFree	Graphical parameter multi-panel plots Set scale free axes [default yes]	[yes|no]
--multi_min	Multi-panel plot 1 visualization threshold. Min normalized gene coverage DEPENDENCY:–scaleFree no [default 0]	[double]
--multi_max	Multi-panel plot 1 visualization threshold. Max normalized gene coverage DEPENDENCY:–scaleFree no [default 100]	[double]
--multiLog_min	Multi-panel plot 2 visualization threshold. Min normalized gene coverage (log10 scale). DEPENDENCY:–scaleFree no [default -1]	[double]
--multiLog_max	Multi-panel plot 2 visualization threshold. Max normalized gene coverage (log10 scale). DEPENDENCY:–scaleFree no [default 3]	[double]
--debug	Dump session and quit
-h, --help	Show help message

Description

The geCNV module aims at comparing the gene sequencing coverage of 2 samples to identify gene CNVs.

The module loads for the two samples the GIP files with the gene sequencing coverage values (.covPerGe.gz files) and calculates for each gene the ratio of the normalized coverage values.

If GIP detected gene clusters (i.e. low MAPQ genes clustered by sequence similarity) this module will also compute and plot the ratio of the cluster coverage score in the two samples.

Example

From the GIP worked example folder execute

giptools geCNV --samples ZK43 LIPA83

This will generate the geCNV output files in the gipOut/sampleComparison folder.

The output consists in four files.

The geCNV.overview.pdf file includes a plot showing the ratio scores of all genes together. If gene clusters are also present, these will be shown in a second, separate pot. For instance, the gene cluster comparison plot for this example is the following:

The geCNV.scatter.pdf file includes a scatterplot representing the normalized coverage score of each gene in the two samples. If gene clusters are also present, these will be shown in a second, separate pot. The gene coverage scatterplot for this example is the following:

The geCNV.multiPanel.pdf file includes two plots showing the gene coverage ratio of all chromosomes in multiple panels. The second plot has the same layout as the first but the values are in log 10 scale, as in this example:

The geCNV.xlsx file reports for each gene the genomic coordinates, the computed normalized coverage scores, the ratio between the two samples, the overlap of the gene with gap and predicted repetitive elements, and if available the gene function. If available, the gene cluster data are reported in a second separate spreadsheet.