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@@ -82,10 +82,12 @@ Running StarSignDNA refit:: | |
starsigndna refit example_data/M_catalogue.txt example_data/COSMICv34.txt --output-folder /test_result --signature-names SBS40c,SBS2,SBS94 | ||
starsigndna refit example_data/tcga_coad_single.vcf example_data/sig_cosmic_v3_2019.txt --output-folder /output --signature-names SBS40c,SBS2,SBS94 --ref-genome | ||
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When the --signature-names option is used, the default number of signature is 3, but we recommend minimum of 5 signatures. | ||
The test data is provided in the example_data folder. To convert *.vcf to a matrix, the user must provide the path to the reference genome using the option --ref-genome. | ||
The user can also provide the distribution of triplets in a reference genome/exome or normal tissue in the same patient (Opportunity matrix) using the option --opportunity-file human-genome/human-exome. | ||
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Running mutational signature de novo algorithm | ||
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@@ -148,6 +150,6 @@ Run denovo using optimal k=4 and λ=0.1:: | |
Contact | ||
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Maintainer Name - [email protected] | ||
Maintainer Name - [email protected] or [email protected] | ||
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