From 228c91fa6fdd13361b0378d95a5a4d2eb90090c8 Mon Sep 17 00:00:00 2001 From: cdbope Date: Thu, 6 Jun 2024 09:48:32 +0200 Subject: [PATCH] update readme --- README.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 01caf59a..7f24d422 100644 --- a/README.rst +++ b/README.rst @@ -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 ----------------------------------------------- @@ -148,6 +150,6 @@ Run denovo using optimal k=4 and λ=0.1:: Contact ------- -Maintainer Name - chrisbop@uio.no +Maintainer Name - chrisbop@uio.no or christianbope@gmail.com