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  • illuminaGA
    Member
    • Dec 2012
    • 71
    #1

    Question about Qiime otu picking

    Dear All

    I am new to 16s sequencing analysis and just finished the otu picking by Qiime.

    Here is the otu pick log file.

    OtuPicker parameters:
    Application:uclust
    Similarity:0.97
    chimeras_retention:union
    enable_rev_strand_matching:False
    exact:False
    max_accepts:20
    max_rejects:500
    new_cluster_identifier:denovo
    next_new_cluster_number:1
    optimal:False
    output_dir:ucrC_all//uclust_ref_picked_otus
    prefilter_identical_sequences:True
    presort_by_abundance:True
    save_uc_files:True
    stable_sort:True
    stepwords:20
    suppress_new_clusters:True
    suppress_sort:True
    word_length:12
    Reference seqs:/home/qiime/Desktop/Shared_Folder/Ref_greengenes_13_8/97ref/97_otus.fasta
    Num OTUs:6546
    Num new OTUs:0
    Num failures:3012933
    Result path: ucrC_all//uclust_ref_picked_otus/seqs_otus.txt

    Seems that I only have 6546/3012933 otu have been picked. Is this normal?

    My libraries were sequenced by Miseq 250x2. I sequenced V4 region only.

    Any help will be appreciated
    Tags: None
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