There are some questions when i using UCHIME algorithms to detect the chimeric sequences in our data. Two outfiles are built (x.uchime.accnos and x.uchime.chimeras) when the analyses finished. In the .chimeras, 11 sequences obtained the positive scores (>0), whether this means the 11 sequences are chimera? However, only 10 sequences are showed in .accnos file. I want to know which result is better.
The sequences in the accnos file are chimeras. The chimeras file should contain the data for all sequences. I would strongly encourage you to look at the uchime manuscritp to understand the algorithm.