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

Join Date: Jan 2013
Posts: 1
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) info is available as it is all proprietary and we are struggling to get anything from them.

Any help/ideas/thoughts/comments welcome.
anniemoo is offline   Reply With Quote
Old 03-31-2015, 11:19 AM   #2
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Location: New England

Join Date: Jun 2012
Posts: 197

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
Location: Belgium

Join Date: Apr 2009
Posts: 24
Default Miseq Reporter Metagenomics and summary

Hi all,

here is some info on Illumina's read classifier for metagenomics:

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 !

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Old 12-05-2016, 07:07 AM   #4
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Location: CT

Join Date: Apr 2015
Posts: 242

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.
Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.
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Old 12-05-2016, 10:36 AM   #5
Location: DE

Join Date: Dec 2012
Posts: 65

^^agreed. mothur is much easier to implement
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