Frequently Asked Questions

How can I cite OncodriveCLUSTL?

You can check OncodriveCLUSTL online publication here. You can cite it as Arnedo-Pac C et al., 2019. OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers. Bioinformatics. pii: btz501. doi: 10.1093/bioinformatics/btz501 .

Where can I download the source code?

The source code of OncodriveCLUSTL is available at bitbucket.org/bbglab/oncodriveclustl. To get the exact same code as in the publication got to https://bitbucket.org/bbglab/oncodriveclustl/commits/tag/1.1.0 .

Which version of OncodriveCLUSTL is running this website?

This website is using OncodriveCLUSTL 1.1.

Which is the mutations file format?

The mutations file is a tabular file with a header that must contain, at least, the following columns:

CHROMOSOME

1, 2,..., X, Y

POSITION

Integer indicating the position of the mutation

REF

Reference nucleotide

ALT

Alternate nucleotide

SAMPLE

Identifier of the sample

The OncodriveCLUSTL available through the web can only be used with mutations mapped to the human reference genome hg19. We assume mutations are mapped to the positive strand. For the web version, mutations file must not be compressed.

Which is the file format of the genomic elements?

The genomic elements file is a tabular file with a header that must contain, at least, the following columns:

CHROMOSOME

1, 2,..., X, Y

START

Starting position of the genomic region

END

Final position of the genomic region

ELEMENT

Identifier of the genomic element

SYMBOL

Symbol of the genomic element

The OncodriveCLUSTL available through the web can only be used with hg19 human reference genome annotations. For the web version, genomic elements file must not be compressed.

Is it possible to do a more customized analysis with OncodriveCLUSTL?

Yes, web application has limited configuration capabilities. Install OncodriveCLUSTL and check all the parameters that can be configured.