After follow the hub with nice results, when I submit my sequences (through get.oturep) 1/3 of the sequences are detected as Chimera by NCBI, so I need to remove manually 5000 sequences.
Do you know any command or tip to obtain a better Chimera detection via Mothur?
Hmm. What are you using to detect chimeras in mothur? Can you provide the command? I assume these are full length sequences?
If they’re MiSeq data, you should be submitting the full dataset (including chimeras) as fastq files to the SRA. Really, even if they’re Sanger, you should be submitting the full dataset.
Pat
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