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update readme
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cdbope committed Jun 6, 2024
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Expand Up @@ -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

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.


Running mutational signature de novo algorithm
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Expand Down Expand Up @@ -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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