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apetkau / orthomcl-pipeline

Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/
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Questions about OrthoMCL software #35

Closed lanlan0210 closed 4 years ago

lanlan0210 commented 4 years ago

Hi，I met a mistake, how can I fix it? Thanks！！！
/orthomcl/orthomcl-pipeline-master/scripts/nml_parse_orthomcl.pl -i ./groups.txt -g genome-groups.txt -s --draw -o orthomcl-stats.txt --genes (What is the file for the -g parameter? -g : A CSV file that contains list of groups to view their ortholog groups. How do I get this CSV file.Is it a generated file or a file that needs to be configured. ) Thank you very much 

apetkau commented 4 years ago

Hello @zhouguilan. The file for the -g parameter is a special file that you have to construct yourself to divide your genomes into the groups you wish to see in the venn diagram.

nepal: VC-25,VC-26,VC-14
haiti: 2010EL-1749,2010EL-1786,2010EL-1796,2010EL-1798,2011EL-2317,2012V-1001,\
3554-08,VC-10,VC-15,VC-18,VC-19,VC-1,VC-6
c6706: C6706

Please refer to https://github.com/apetkau/microbial-informatics-2014/tree/master/labs/orthomcl#step-8-venn-diagram-of-orthologs for more information.