I apologize if this is redundant, but I couldn't find exactly what I was looking for in other posts.
I have 8 assemblies. I've mapped the contigs from four of the assemblies to the contigs of the other four, like so:
So I have four BLAST output files.
What I want to do is make four Venn diagrams with the circles being the "S" and "W" contigs, and the overlapping portion representing the number of contigs that aligned within certain parameters. Is this possible? I feel very dumb, but I just can't figure out how to make it work.
•
written
by
sturne29 •
One way to do this would be to compute the number of nucleotides each pair of contigs has in common (maybe taking into account only nucleotides that form a stretch of length above a threshold or only counting some HSPs) and use this to draw the Venn diagram.
What data specifically would I be using to make this? Just the numerical data (# of nucleotides in S and W, then the middle is the % that overlap)?
Yes, you can use nucleotide counts and in that case, the overlap should also be expressed in number of nucleotides. Alternatively, you can use percentages. You just need to be consistent. Note that not all functions/programs draw proportional diagrams (i.e. with areas proportional to the size of the sets).
Still not sure what this venn diagram would represent.
@sturne29: We have no idea about the constituents of these four groups. Are they roughly same size? Are these assemblies of the same data? What kind of blast was used and what parameters were used? LASTZ may be more appropriate if these are large chromosome sized pieces.
Log in to answer this question.
Can you clarify what it is you want to represent by such a diagram? How similar/different are J/O/W/S considering the parameter chosen?
J and O are months, July and October; represent when the sample was taken. At the moment, I'm not too concerned about trying to figure out differences between communities based on time, so that part isn't really too important. S and W stand for sediment and water column, which is what I'm actually interested in. The whole point is basically to show the pool of "overlapping" (i.e., aligning within certain parameters) contigs, because one of the points I'm interested in is organisms found in both habitats.
So this is a metagenomic dataset.
Then rather than looking at just blast you are more interested in organisms that are in the dataset. You may want to look into MEGAN since that would probably be useful here.
Hi Dear Friend, maybe this could help : https://omictools.com/vennblast-tool