Processing OrthoMCL output file, "groups.txt" to create a venn diagram
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9.0 years ago
jc_0919 • 0

Hi I am wondering if anyone here can help me with the processing of my results obtained with the software OrthoMCL. I used this software to find orthologous protein sequences between several genomes of interest and got a resulting file at the end called "groups.txt" that looks as follows:

ort_1000: f79|KGY61984.1_3 f79|KGY61985.1_4 f79|KGY61986.1_5
ort_1001: cbg|648.25.peg.1151 cbg|648.25.peg.1292 cbg|648.25.peg.2512
ort_1002: f78|KGY70202.1_1 f78|KGY70203.1_2 f78|KGY70204.1_3
ort_1003: 838|WP_039039924.1_1 838|WP_042016014.1_1 f78|KGY71286.1_1162

Can someone please explain to me how to go about creating a venn diagram using this file that would show the core genome (i.e. all orthologs shared) between the different species. Thank you so much :-)

genome-comparison OrthoMCL Core-genome orthologs • 3.7k views
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I was easier for me to start if your headers

ort_1000: f79|KGY61984.1_3 f79|KGY61985.1_4 f79|KGY61986.1_5

were

1000 (number only): 79(number only) | gene_id (number/text)

and no ids like cbg| you should give organism number instead.

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