chimera break point

Theory behind mothur
1

After running UCHIME I was curious if it is possible to determine the chimera break point in the chimeric sequences. Any suggestions on determining this would be much appreciated.

Thanks!
Julia

2

Those data should be in the uchime.chimera output file

3

I must be missing something in the output file then. Which column represents the break point?

Thanks!

4

Huh, sorry - I thought the output file had that information. We regurgitate the output from Edgar’s Uchime, but it doesn’t seem that he provides that information. Not sure why… You might try setting chimealns=T and see what happens although I suspect that will give you way more than you want.

Pat