Question: KEGG pathway file for running genome music path-scan
gravatar for Chirag Nepal
27 days ago by
Chirag Nepal2.1k
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, , 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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1459 users visited in the last hour