16S Metagenomics Ion Torrent thermo scientific

Fabien · 04-09-2019, 11:37 AM

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

...

SylvainM · 10-03-2019, 09:12 AM

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

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
16S Metagenomics Kit for Ion Torrent	JenBarb	Ion Torrent	11	02-12-2019 08:43 AM
Ion Torrent Metagenomics flows	Serratiam	Ion Torrent	1	02-11-2019 07:03 AM
Scientist III, BioInformatics - Thermo Fisher Scientific	ThermoRecruiter	Industry Jobs!	0	12-08-2014 02:16 PM
Ion Torrent $1000 Genome!? Benchtop Ion Proton Sequencer	aeonsim	Ion Torrent	88	10-28-2012 05:50 AM

04-09-2019, 11:37 AM	#1
Fabien Junior Member Location: chile Join Date: Apr 2019 Posts: 1	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 ...

10-03-2019, 09:12 AM	#2
SylvainM Junior Member Location: Limoges Join Date: Feb 2019 Posts: 2	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