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Old 03-31-2015, 10:38 AM   #1
anniemoo
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Location: Pretoria, South Africa

Join Date: Jan 2013
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Default MiSeq Reporter Metagenomics Workflow

Hey there

Has anyone used the MiSeq Reporter Metagenomics Workflow before? Is it worth it? Or is QIIME the absolute way to go?

My problem with the MSR workflow is the fact that I don't know what happens between purity filtering fastq file generation and the start of the taxonomic classification (in terms of quality trimming/chimera checking etc)...no info is available as it is all proprietary and we are struggling to get anything from them.

Any help/ideas/thoughts/comments welcome.
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Old 03-31-2015, 11:19 AM   #2
microgirl123
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We tell all of our users that it's nice and generates pretty pie charts, but you have to actually do the data analysis yourself. There is absolutely no documentation about how the data is quality checked available. It's also not comparing your data to a full 16s dataset - just an "Illumina curated" subset of Greengenes (I think). I have no idea how you could publish data from MSR. It's great for a quick undergrad poster presentation, but other than that I don't think it's worth much unless Illumina is much more forthcoming about the analysis.
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Old 12-02-2016, 01:20 PM   #3
BioGenomics
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Default Miseq Reporter Metagenomics and summary

Hi all,

here is some info on Illumina's read classifier for metagenomics: http://support.illumina.com/help/Bas...thods%7C_____1


I was wondering if anybody had a script/tool to merge all the individual results from MSR Metagenomics into a nice summary table to be used in VEGAN or Calypso ? In BaseSpace, the aggregate results csv is what you need, but it is not implemented in MSR tool...

thanks !

Greg
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Old 12-05-2016, 07:07 AM   #4
thermophile
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I completely agree with microgirl. Why spend thousands generating data if you are going to trust a pie chart from a black box.

I prefer mothur to qiime.
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Old 12-05-2016, 10:36 AM   #5
lac302
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^^agreed. mothur is much easier to implement
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