Question: Making a Venn Diagram Using BLAST Results?
1
gravatar for sturne29
2.8 years ago by
sturne2910
sturne2910 wrote:

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:

  • JW1 contigs mapped to JS1 contigs
  • JW2 contigs mapped to JS2 contigs
  • OW1 contigs mapped to OS1 contigs
  • OW2 contigs mapped to OS2 contigs

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.

ADD COMMENTlink modified 2.8 years ago by Jean-Karim Heriche18k • written 2.8 years ago by sturne2910
1

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?

ADD REPLYlink written 2.8 years ago by genomax65k

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.

ADD REPLYlink written 2.7 years ago by sturne2910

So this is a metagenomic dataset.

one of the points I'm interested in is organisms found in both habitats.

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.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax65k
1

Hi Dear Friend, maybe this could help : https://omictools.com/vennblast-tool

ADD REPLYlink written 2.8 years ago by Farbod3.2k
0
gravatar for Jean-Karim Heriche
2.8 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

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.

ADD COMMENTlink written 2.8 years ago by Jean-Karim Heriche18k

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)?

ADD REPLYlink written 2.8 years ago by sturne2910

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).

ADD REPLYlink written 2.8 years ago by Jean-Karim Heriche18k

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.

ADD REPLYlink written 2.8 years ago by genomax65k
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: 1867 users visited in the last hour