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4.8 years ago
Chirag Nepal ★ 2.3k
I am using genome music path-scan to find signifiacntly mutated pathways.
genome music path-scan --gene-covg-dir gene_covgs --bam-list $bamList --pathway-file $pathwayKEGGFile --maf-file $maf --output-file $pathwayOutputFile -bmr 1.8E-6
The program requires KEGG pathway file. KEGG file used by music can be found here, https://raw.githubusercontent.com/ding-lab/parse-kegg/master/all_pathway_files/KEGG_052412 , but it is not updated from 2012. Can somebody share (if they have updated one) or help me to prepare this file in required format.
There is probably no update since 2012. KEGG FTP is not public anymore, but works with subscription since 2011. So I think 2012 was the last public available file from FTP.