MutSigCV
The simplest way to run MutSigCV is through genepattern.org.
At the top of the page click Run > Public Server.
If you haven’t already, register for an account on the website.
Once you’ve logged in:
- Click Browse Modules
- Scroll down to mutational significance analysis
- Click MutSigCV
Generating the mutation table file
The mutation table file is just a MAF file, so just save the MAF file downloaded through TCGAbiolinks locally.
write.table(maf, "~/Downloads/TCGA_SKCM.maf", row.names = F, sep = '\t', quote = F)
Running MutSigCV
After saving the MAF file locally, upload it to the mutation table file input by clicking the Upload File button.
The remaining inputs to MutSigCV include 3 reference files, which are listed below:
coverage table file: ftp://ftp.broadinstitute.org/pub/genepattern/example_files/MutSigCV_1.3/exome_full192.coverage.txt
covariates table file: ftp://ftp.broadinstitute.org/pub/genepattern/example_files/MutSigCV_1.3/gene.covariates.txt
mutation type dictionary: ftp://ftp.broadinstitute.org/pub/genepattern/example_files/MutSigCV_1.3/mutation_type_dictionary_file.txt
Fill out the 2 remaining inputs as follows:
output filename base: TCGA_SKCM
genome build: hg19
Click Run!