Question: Processing OrthoMCL output file, "groups.txt" to create a venn diagram
0
gravatar for jc_0919
4.9 years ago by
jc_09190
Mexico
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

were

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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2034 users visited in the last hour