KEGG pathway file for running genome music path-scan
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 !!
• 2,051 views
•
link
written
by
Chirag Nepal
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Error when running Genome MuSiC: no smg genes
written by C Wang •
-
Are there recommended steps if MuSiC reports too many significantly mutated genes
written by Collin
-
genome music bmr calc-covg [Run in parallel]
written by Chirag Nepal
-
Music Path-Scan Problem
written by zhouyunyun11 •
-
Question About The Music Pathscan Fdr Value
written by xiaoqiaoliu •
-
Calcbmr Of Music(0.4) Error: Error Runing Command Joinx1.6
written by Ryo Murasaki •
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.