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Old 01-06-2015, 09:08 AM   #1
illuminaGA
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Location: Atlanta

Join Date: Dec 2012
Posts: 54
Default 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
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