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How to obtain the statistics of the OrthoMCL output file

Hey guys,

I been doing some OrthoMCL analyses (stand-alone version) with 4 different species. Now I would like to build a venn diagram showing the statistics of the comparison (e.g. numbers of clusters shared by all the species, number of clusters only shared by two species, and so forth). I haven't came across a way to split the "groups.txt" output file to get this numbers.

Any thoughts?

Thanks in advance,
J.

orthomcl
• 4,439 views • link
updated by Ram Ram • written by javo.vc • javo.vc

Does the groups.txt file follow the format of each ortholog group being listed at a single line? If yes, are your protein IDs species specific? If yes, then getting these statistics ought to be rather easy with e.g. awk

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written by 5heikki 5heikki

No, that's the problem, species are mixed through the file

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written by javo.vc • javo.vc

And yes, my protein ID's are species specific

• 0 views • link
written by javo.vc • javo.vc

1 answer

Try http://bioinformatics.psb.ugent.be/webtools/Venn/ ....nothing more simple than this, but for this you need to use excel and note++. first. Let me now if you still struck up.......I will elaborate........

• 1 views • link
updated by Ram Ram • written by amanjain • amanjain

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