FORUMOTU table
Genevieve asked 6 months ago



  • Hi, 
    how can I get OTU table from Vsearch clustering ?

    5 Answers
    jrosner Staff answered 6 months ago



  • Hi Genevieve, Vsearch has three options for outputting an OTU table.
    From the VSEARCH documentation:

    --biomout filename

    Generate an OTU table in the biom version 1.0 JSON file format

    --mothur_shared_out filename

    Output an OTU table in the mothur ’shared’ tab-separated plain text format.

    --otutabout filename

    Output an OTU table in the classic tab-separated plain text format as a matrix containing the abundances of the OTUs in the different samples.
     
    Let me know if this helps!

    Genevieve replied 6 months ago

    Hi,
    I’m not sure to understand. I’m using Vsearch in Galaxy. I would like to cluster my sequences to OTUs so i’m using Vsearch clustering and I don’t see the options of you talking about. Bio-informatic is new for me.

    jrosner Staff replied 6 months ago

    ah ok. you’re using Galaxy.
    I had a look as well and I don’t see the option either.
    Let me look around and see if there’s a workaround for this.

    Genevieve replied 6 months ago

    Hi,
    sorry for the delay I tried many things at the same time. I succeeded to obtain an OTU table with your instructions. I installed Vsearch on windows (–mothur_shared_out filename) thank you. Now I tried to use my Output OTU table in the mothur ’shared’ tab-separated plain text format in Mothur (Galaxy) without success. When I try to chose a file I always have No mothur.otulabels dataset available. Do i need to do a another step before to start analyse with mothur ?

    flefebvre Staff answered 6 months ago



  • Hi Genevieve, the stand-alone vsearch at usegalaxy.org is outdated (2015) and  –otutabout that Jamie mentioned was introduced in 2016 only.
    You would probably be able to use the windows version of vsearch directly:
    https://github.com/torognes/vsearch/releases
    vsearch cluster is also a method available in “NGS:Mothur” “Cluster”.
    Could you perhaps let us know what your overall goal and current strategy is? Are you trying to follow a Galaxy tutorial?
     
     

    Genevieve replied 6 months ago

    I tried Mothur – cluster- but I got an error message
    I think its because I didn’t put the right file. On the cluster based on option i chose Fasta Vsearch (I put a fasta file with all my sample) and after for the clustering method I chose the abundance-base greedy clustering agc (vsearch) and i need to chose a fasta file after. I don’t know if I chose the right file.

    Genevieve answered 6 months ago



  • Thank It works well with Vsearch on windows 🙂

    Genevieve answered 6 months ago



  • I still have question about OTU table in Vsearch. Can someone help me ?

    Genevieve replied 6 months ago

    When I do clustering in Vsearch I would like to obtain a count_table (as Mothur do). I want to know for each representative sequences (cluster) how much sequences from each of my differente sample I have. Is it clear ?

    Here the script I use ( Vsearch windows) for my clustering
    vsearch –cluster_size 301_3315_5028_6584.ITS2.fasta –id 0.97 –sizein –sizeout –centroids cluster_test.fasta –biomout fungal_test.JSON –mothur_shared_out fungal_mothur_test.txt –otutabout Fungal_test.txt

    Thanks in advance

    jrosner Staff answered 6 months ago



  • Hi Genevieve,
    I think it would be best for you to have a one-on-one session with a member of our team.  This can be done over the phone or video conference and (given the scope of the problems you’ve encountered) should make it things faster and easier.  This way we can get an idea of your overall goal and the best strategy to achieve your results without all of the back and forth and waiting time in between.
    How does this sound?

    Genevieve replied 6 months ago

    Yes I think it will be the best. How it works to cedule a non-on-one session with a member of your team ? Also do you think I can have someone who speak french ?

    jrosner Staff replied 6 months ago

    A member of our team will reach out to you via email to schedule the appointment.
    And we’ll do our best to find someone who speaks French.

    Cheers!

    Genevieve replied 6 months ago

    Thank 🙂