Galaxy tool preview

Venn Diagram (version 0.0.3)
Tabular file (uses column one), FASTA, FASTQ or SFF file.
Sets
Sets 0

TIP: If your data is in tabular files, the identifier is assumed to be in column one.

What it does

Draws Venn Diagram for one, two or three sets (as a PDF file).

You must supply one, two or three sets of identifiers -- corresponding to one, two or three circles on the Venn Diagram.

In general you should also give the full list of all the identifiers explicitly. This is used to calculate the number of identifers outside the circles (and check the identifiers in the other files match up). The full list can be omitted by implicitly taking the union of the category sets. In this case, the count outside the categories (circles) will always be zero.

The identifiers can be taken from the first column of a tabular file (e.g. query names in BLAST tabular output, or signal peptide predictions after filtering, etc), or from a sequence file (FASTA, FASTQ, SFF).

For example, you may have a set of NGS reads (as a FASTA, FASTQ or SFF file), and the results of several different read mappings (e.g. to different references) as tabular files (filtered to have just the mapped reads). You could then show the different mappings (and their overlaps) as a Venn Diagram, and the outside count would be the unmapped reads.

Citations

The Venn Diagrams are drawn using Gordon Smyth's limma package from R/Bioconductor, http://www.bioconductor.org/

The R library is called from Python via rpy, http://rpy.sourceforge.net/

This tool uses Biopython to read SFF files. If you use this tool with SFF files in scientific work leading to a publication, please cite the Biopython application note:

Cock et al 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.