KEGG pathway file for running genome music path-scan
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4.8 years ago
Chirag Nepal ★ 2.3k

Hi all,

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.

thanks !!

MuSic KEGG • 1.3k views
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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.

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