Venn Diagram From Cap3 Output
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8.8 years ago

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

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8.8 years ago
Prakki Rama ★ 2.6k

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

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

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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!

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8.8 years ago
Martombo ★ 3.0k

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.

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

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There is also Venny for 4 sets.

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Venny is what Prakki Rama was referring earlier...

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