Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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




    ...

  • #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

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X