Venn Diagram From Cap3 Output

Question

[upendrakumar.devisetty]

Hi, I have generated a cap3 consensus assembly from three different assemblers (velvet/trinity/tophat). Now i would like to find out how many of those contigs are either unique, shared by two or by three assemblers. Right now i have a log file that indicates contig information and the transcripts contributed by those contigs. Could somebody help me making a venn diagram for this. Here is the log file..

Contig575       BRME_20693+,comp2892494_c0_seq1+
Contig574       BRME_20689+,TCONS_00061423+,TCONS_00061424+
Contig577       BRME_20739-,TCONS_00051195+,TCONS_00051196+,comp257652_c0_seq3+

BRME stands for velvet assembly, comp stands for trinity and TCONS stands for trinity asseblies.

Thanks Upendra

Answer 1

[Prakki Rama]

May be this might help you.

grep 'comp' inp2.txt | cut -d " " -f 1 >comp.txt
grep 'BRME' inp2.txt | cut -d " " -f 1 >BRME.txt
grep 'TCONS' inp2.txt | cut -d " " -f 1 >TCONS.txt

put the contig name in venny. Should look like this

[upendrakumar.devisetty]

Thanks. I didn't realized that it was so easy. I finally got what i wanted....

[InterestedScientist]

Venny was down today... In any event, I would highly recommend I would highly recommend VENDIS.

It just came out and it's really quite good!

Answer 2

[Martombo]

Since you have only three different groups you can easily make a venn diagram with the areas proportional to the number of elements shared or unique for each group. Have a look at biovenn.

To use this tool you have to produce the lists of contigs as explained by Prakki Rama.

[upendrakumar.devisetty]

Thanks for the tool. I was not aware of that too.. It worked great....

[zx8754]

There is also Venny for 4 sets.

[upendrakumar.devisetty]

Venny is what Prakki Rama was referring earlier...