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Old 08-08-2017, 12:44 AM   #1
odyssey
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Question UniFrac analysis for Sanger and 454 pyroseq data

Hi, all!
I have a dataset from Sanger (12 seqs ~350-500bp) and 454 sequencing (32000 seqs (140 OTUs) ~500bp).

And here is a question:
It's possible to compare OTUs seqs from 454 with Sanger by weighted\unweighted UniFrac analysis?

And one more question: It's correctly to do this if I have so different size of datasets - 12 seqs vs. 140 OTUs? Could I say that my 12 Sanger seqs are equivalent to OTUs in metagenome?

Thanks,
Kind regards!
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Old 08-23-2017, 07:28 AM   #2
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Could I say that my 12 Sanger seqs are equivalent to OTUs in metagenome?
I'd be hesitant in saying so. Different platforms employ different strategies to generate data. Even if you'd sent same samples in pyro and sanger machines it's possible to not have same thing sequenced equally.
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Old 08-23-2017, 07:54 PM   #3
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Thanks for your answer, bio_informatics!

Could you advise me something in this case? May be there is any way to compare my datasets?
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Old 08-24-2017, 03:05 AM   #4
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Originally Posted by odyssey View Post
Thanks for your answer, bio_informatics!

Could you advise me something in this case? May be there is any way to compare my datasets?
1- I'd take FASTA file before chimera checks from both the runs, merge, remove chimeras and proceed for classification.

2- Maybe reaching out to QIIME folks on their forum would be fruitful.
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Old 08-24-2017, 11:43 PM   #5
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Ok, thanks a lot for your advice
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Old 08-25-2017, 07:24 AM   #6
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Originally Posted by odyssey View Post
Hi, all!
It's possible to compare OTUs seqs from 454 with Sanger by weighted\unweighted UniFrac analysis?
I've not done Unifrac analyses but one issue while merging OTUs from different runs is that there can be duplicate OTUs.
That's why I suggested to merge FASTA from both runs, then cluster, remove chimera (or remove chimera then cluster).
I hope this makes sense. Sorry, for not clarifying earlier.
Good luck.
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