Sequence grouping of the seqs.fna file

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Deb Colman

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Nov 15, 2016, 12:21:22 PM11/15/16
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I'm stuck in the 454 sequence analysis of 7 different environments. The objective is to have the OTUs of the 7 samples separately and then compare.
I have an initial fasta file (where the 454 sequences of the 7 environments are mixed). I already ran the mapping file and split_library validation. From this second script, I got the seqs.fna file. And it is from there where I suppose that I must divide the samples corresponding to their origins. But I do not know how to do it.

In turn, I also followed the instructions of the tutorial, so the next step was pick_de_novo_otus.py. But the otus he generated is a mixture of all environments.

I hope you can help me again

Thank you!!

zech xu

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Nov 15, 2016, 5:34:16 PM11/15/16
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Hi Deb,

You should separate your samples before OTU picking. You can run whatever OTU picking method (open reference, closed reference, de novo) you'd like to create an OTU table for all the samples. And then you can compare if there is any diffference between samples from different environments.

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