Check for chimeras in Costello stool analysis

Commands in mothur
1

Hi,

I noticed that a few changes were made in the way to check for chimeras in the Costello stool analysis. It is suggested to use both chimera.slayer and chimera.uchime. In the example, after using those two methods, the potential chimeric sequences detected with chimera.uchime are removed, but not the ones detected with chimera.slayer. I guess this step should happen before running the chimera.uchime? Is there an easy way to know how many sequences were detected as chimeras by both program? Is it possible to remove the chimeric sequences from both accnos files at the same time with remove.seqs?

Thank you,

Nathalie

2

no, no - those are listed as potential options - the goal isn’t to have people do both options. pick one and run with it. we are currently suggesting using uchime with reference=self