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LMM 01-10-2018 03:03 PM

454 data analysis in Qiime1
 
Hello
I analysing 454 data using Qiime1. I have 4 .fna files that seem to be split into 2 forward read and 2 reverse read files. At what point in the pipeline should I combine them? Before demultiplexing? Combine the OTU tables?
Thanks
Laura

thermophile 01-11-2018 05:59 AM

I don't know qiime well (only used enough to know that I strongly prefer mothur). So can't tell you exactly where to combine but you can't combine OTU tables if you do denovo clustering. In mothur, I combined after demultiplexing, sequence qc, and chimera checking but before aligning and clustering into OTUs

LMM 01-11-2018 06:30 AM

Ok thank you!


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