5. Using iCOMIC for cTaG and NBDriver tools¶
5.1. cTaG¶
cTaG
(classify TSG and OG) is a tool used to identify tumour suppressor genes (TSGs) and oncogenes (OGs) using somatic mutation data. The cTaG model returns the list of all genes labelled as TSG or OG or unlabelled along with predictions made by each model and whether the gene is among the top predictions.
5.1.1. Input Requirements¶
A maf
file is required to run the cTaG tool. A maf file can either be generated from the DNA-Seq output vcf file in the results tab or browsed locally. Apart from that, you can mention the parameters
required to run the cTag in the parameters option provided.
5.1.2. Initialization of the analysis¶
You can click on the run
button to initialize the analysis, once the necessary files have been uploaded.
5.1.3. Results¶
Once the analysis is completed, you can click on the Results
button to view the results
5.2. NBDriver¶
NBDriver
(NEIGHBORHOOD Driver) is a tool used to differentiate between driver and passenger mutations using features derived from the neighborhood sequences of somatic mutations. NBDriver returns a list of all mutations labelled as Driver
or Passenger
.
5.2.1. Input Requirements¶
In order to run NBDriver, the user needs to download the hg19 reference genome from this link and put it in the "/icomic/NBDriver_iCOMIC/" directory
A vcf
file is required to run NBDriver. The vcf file can either be browsed from the DNA-Seq output directory or locally.
5.2.2. Initialization of the analysis¶
You can click on the run
button to initialize the analysis, once the necessary files have been uploaded.
5.2.3. Results¶
Once the analysis is completed, you can click on the Results
button to view the results