Question: KEGG pathway file for running genome music path-scan
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gravatar for Chirag Nepal
27 days ago by
Chirag Nepal2.1k
Copenhagen
Chirag Nepal2.1k wrote:

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 !!

kegg music • 80 views
ADD COMMENTlink modified 27 days ago • written 27 days ago by Chirag Nepal2.1k

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.

ADD REPLYlink written 27 days ago by b.nota4.3k
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