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Old 04-09-2019, 10:37 AM   #1
Fabien
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Location: chile

Join Date: Apr 2019
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Unhappy 16S Metagenomics Ion Torrent thermo scientific

Hi,

I am analyzing statistical data obtained from reads generated by the Ion Torrent sequencing method using the 16S Metagenomics Kit of thermo scientific for the the first time.

An equivalent of OTU table has been generated by the Software Ion Reporter (Thermo Scientific). I did not this part.

So I have to realize the statistical part from the OTU-table.

But I do not understand the OTU table and particularly the taxonomy assignment:

You can have :
1) «slash calls » which would correspond to not identified species
2) " (genus level ID only) » that will be correspond to the sum of all the species of the genus. but when I sum the count, it is not correspond... So I do not understand ...

I put an example for species of the bacteroides, I have:

(slash calls) 96
acidifaciens 4.405
sp. 2.962
(genus level ID only) 2.493

As you can see the count of "genus level ID only" do not correspond to the sum of the bactericides species...

someone can help me please....

Thank you for you answer...

Fab




...
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Old 10-03-2019, 08:12 AM   #2
SylvainM
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Location: Limoges

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Hi Fabien,

The "genus level only" correspond to reads that couldn't be identified deeper in the taxonomy.
So in fact it is not an addition of reads. You have to consider this as an other category of reads identification.

In your example, if you stop a the genus level you have to add the reads of the slash calls + acidificans + other species identified in the genus + sp + genus level only.
If you want to look at the species level, those reads will not enter in your datas as it stopped at the genus level.

Hope I have been clear enough.

Sincerely,

Sylvain
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