Venn Diagrams and Species

Commands in mothur
1

Hi All,

I have a question concerning the venn() command. Is it possible to determine which species, not just the species numbers, are shared and not shared between two or more groups when generating Venn Diagrams? In other words, is there a way to determine the classification of the species (as is reported in the summary file of the classify.seqs command) that are shared and not shared between the groups?

Thanks for the help in advance!

-George

2

I think what you are looking for is the get.sharedseqs command. It is like a text output of the venn diagram. It will output the sequences contained in the otus in the different pieces of the diagram. You will need to use the unique and or shared parameters to enter the groups you would like the info for.

3

Hey all, I am in possession of a fasta file with approximately 1100 unique names, ( i.g. B10988 ), and I want to generate a tab delimited file with just those names in a continuing column ( without sequences ). This is so I’m able to then build a “group” file for mothur and run multi sample research ( the different names refer to microbial population samples from 6 different sites ).

I can not seem to think about a technique to do this in text wrangler, word, excel, ect… So any recommendation is much appreciated. Generally if you have suggestions for a programme that’s good at formatting and concatenating different sequence files ( fasta, nexus, phylip, ect. ) that would be great too.

4

try…

grep “>” sequences.fasta | cut -c -2 > sequences.accnos

5

Thanks it works :smiley: