Question: How to get gene abundance visualization and venn diagram from PROKKA output file?
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gravatar for nisrinalulu
12 months ago by
nisrinalulu10
nisrinalulu10 wrote:

Hi Everyone,

I hope you all doing well.

I work with metagenomics data from soil samples and have annotated it using PROKKA. I need visualize PROKKA output to get gene abundance visualization and venn diagram. Do you have a suggestion for me what software or what R packages that I can use to get gene abundance visualization and venn diagram from PROKKA output?

Thank for your help and time.

Regards, Lulu

metagenomics R • 590 views
ADD COMMENTlink written 12 months ago by nisrinalulu10

what exactly do you want to see visualised in a venn diagram?

if you're not afraid of some file reformatting, this webtool might be of use?: http://bioinformatics.psb.ugent.be/webtools/Venn/

ADD REPLYlink written 12 months ago by lieven.sterck10k

Dear lieven.sterck,

Thank you for your reply and your web tool recommendation. The web tool that you mentioned looks easy to use but I have to convert the file format.

I want to see gene in venn diagram among 4 my samples.

Do you have another software recommendation?

Thank you

ADD REPLYlink modified 12 months ago • written 12 months ago by nisrinalulu10

well, in any case if you want to represent it in a venn diagram, you will need some way of linking the genes to each other (based on naming for instance, but that will likely not work in this case).

ADD REPLYlink written 12 months ago by lieven.sterck10k

I see. Thank you for your reply. I think I can use R packages to produce gene abundance visualization and venn diagram from my data set, but I still looking for the best packages that I can use to produced it.

ADD REPLYlink written 12 months ago by nisrinalulu10

Dear lieven.streck,

Do you have a tutorial or paper to reformatting PROKKA output file to suitable format file for http://bioinformatics.psb.ugent.be/webtools/Venn/?

Thank you

ADD REPLYlink written 12 months ago by nisrinalulu10

no sorry, don't have such a document.

however, input is pretty simple, it's just a list of IDs (== elements you want to compare, can be anything actually) in plain text format.

key issue remains that you will need to find some way to link the genes (?0 to each other. perhaps do a AllVsAll blast search and take the best hits? I assume that simply taking the predicted gene IDs will not do it as you can't be sure they point to the same gene.

ADD REPLYlink written 12 months ago by lieven.sterck10k
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