I’m now trying to remove chimera sequences on my data. I’m using Vsearch with the default parameters with the Uchime reference data set and I lost almost all of my sequences (ITS2 fungal sequences) from my sample. Its not normal ? I’m not familiar with all the setting. Can anyone hepl me ?
If you send me the parameters you used while running Uchime, I may be able to help you.
thankl finaly I found the solution
Would you be able to post your solution here please? It might help other users with the same problem.
Yes of course
I forgot to specify the Select output formats at the end (–nonchimeras).