I am wondering as to what percentage the Chimera.uchime command recovers chimeras. The wiki and other sources advise not to blindly discard all sequences flagged as chimeras by tools such as the Chimera.uchime command in mothur, and that you should manually check if they really represent PCR artifacts. Now I have been searching the literature as to how to do this, but I can’t seem to find an answer. Is there anybody that can find the time to explain to me how to manually check if a sequence is chimeric? Or point me in the right direction with an article if there is one?
You would really help me a lot with my project!
a student looking for guidance