Question: Venn Diagram From Cap3 Output
2
gravatar for upendrakumar.devisetty
5.9 years ago by
United States
upendrakumar.devisetty360 wrote:

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

• 2.1k views
ADD COMMENTlink modified 5.9 years ago by Martombo2.6k • written 5.9 years ago by upendrakumar.devisetty360
4
gravatar for Prakki Rama
5.9 years ago by
Prakki Rama2.4k
Singapore
Prakki Rama2.4k wrote:

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

ADD COMMENTlink written 5.9 years ago by Prakki Rama2.4k

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

ADD REPLYlink written 5.9 years ago by upendrakumar.devisetty360

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

http://kislingerlab.uhnres.utoronto.ca/projects/VennDIS_v1.0.zip

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

ADD REPLYlink written 5.0 years ago by InterestedScientist30
2
gravatar for Martombo
5.9 years ago by
Martombo2.6k
Seville, ES
Martombo2.6k wrote:

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.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Martombo2.6k

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

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by upendrakumar.devisetty360

There is also Venny for 4 sets.

ADD REPLYlink written 5.9 years ago by zx87549.0k

Venny is what Prakki Rama was referring earlier...

ADD REPLYlink written 5.9 years ago by upendrakumar.devisetty360
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