Question: Processing OrthoMCL output file, "groups.txt" to create a venn diagram
gravatar for jc_0919
4.9 years ago by
jc_09190 wrote:

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 :-)

ADD COMMENTlink written 4.9 years ago by jc_09190

I was easier for me to start if your headers

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


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

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

ADD REPLYlink written 4.8 years ago by Nari870
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