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Old 01-10-2018, 04:03 PM   #1
LMM
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Default 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
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Old 01-11-2018, 06:59 AM   #2
thermophile
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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
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Old 01-11-2018, 07:30 AM   #3
LMM
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Ok thank you!
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