I'm making 2 Metagenomics pipelines (one for WGS and one for 16S) and I just found out about Chimeras and I think I understand what they are.
Chimeric sequences are products when 2 halves of a PCR product "link" together to form one sequence. This is a problem because the sequence can then be assigned as a different (wrong) sequence.
But I don't (at all) see this as a problem for 16S, because this sequence is so short you'll allow a very small mismatch ratio (0-1) so you won't see anything.
The people I work with have never looked for Chimeric sequences and say that it isn't really a problem here even for WGS. Are they wrong? Why do I want to really search for chimeric sequences? What kind of tool do you advise to use? And am I wrong about the 16S approach?
Thanks for reading and if you reply, thank you even more.
Chimeric sequences are products when 2 halves of a PCR product "link" together to form one sequence. This is a problem because the sequence can then be assigned as a different (wrong) sequence.
But I don't (at all) see this as a problem for 16S, because this sequence is so short you'll allow a very small mismatch ratio (0-1) so you won't see anything.
The people I work with have never looked for Chimeric sequences and say that it isn't really a problem here even for WGS. Are they wrong? Why do I want to really search for chimeric sequences? What kind of tool do you advise to use? And am I wrong about the 16S approach?
Thanks for reading and if you reply, thank you even more.
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