FAQ

Data Import 

How do I import data in VCF format?

VCFs must first be converted to MAF format.

See usage/importing_data for detailed instructions.

If you are not, please contact us.

We are currently working on building better workflows for importing VCFs to CRUX.

Why can I not import GDC MAF / annotation files?

The import of GDC data into CRUX most commonly fails due to confusion caused by the ‘annotations.txt’ file that is automatically downloaded alongside MAF files.

annotations.txt is NOT a valid clinical annotations file, it only contains file-level metadata.

If your upload fails, even when you try to upload the GDC MAF files alone, please screenshot the error message and contact us so we can resolve the issue.

A list of genes which are frequently mutated in somatic cancer datasets but that are unlikely to drive disease. These genes can be excluded from analysis in CRUX. The genelist is described in the somaticflags package.

Why is the text in my figures so small?

Most visualisation modules have options to set text-size. Sometimes increasing the font-size will cause parts of the text to be cut off. When this happens, you have two options. Look for an option to increase margins (e.g Margin: genes if working with an oncoplot). Alternatively, keep the font-size small, download the plot in a vector-based format such as a PDF (Illustrator) or SVG (Inkscape) and edit the text size in an 3rd party program.

Hopefully, we will one day have the options to set ‘Margins’ for all plots.

FAQ

Data Import 

How do I import data in VCF format?

Why can I not import GDC MAF / annotation files?

Analysis 

What are ‘dubious genes’?

Why is the text in my figures so small?

Tool development 

I have an idea for a new feature. Who should I tell?

Where do I report bugs and other odd behaviour?

Miscellaneous 

My question isn’t here. What do I do?