Dataset: OTU table for 18S rRNA gene tag sequences from DNA and RNA
Deployment: SPOT_Yellowfin_Cruises

These data were published in Hu et al., 2016.

This dataset is a raw output operational taxonomic unit (OTU) table generated by processing and clustering raw 18S rRNA gene tag sequences from DNA and RNA. The numbers in each column represent the number of sequences from that sample belonging to a given OTU (row), with the last column listing the taxonomic ID assigned to each OTU. The raw sequence data can be found in the NCBI SRA database under accession number SRP070577 with the associated BioProject PRJNA311248.  Metadata for these sequences can be found in the dataset:
”18S rRNA gene tag sequences from DNA and RNA": https://www.bco-dmo.org/dataset/745527

Nucleotide bases with a Q score lower than 20 for the last 30 bp of each sequence were trimmed. Paired-end sequences were merged using FLASh (Magoc and Salzberg 2011) with a minimum of 10 bp and maximum of 150 bp overlap between each sequence pair. Sequences shorter than 350 bp, longer than 460 bp, or which had an average quality score lower than 25 were discarded using QIIME v1.8 (Caporaso et al. 2010). Chimeric sequences were identified and removed, by either de novo or reference-based chimera checking (identify chimeric seqs.py in QIIME, intersection method). 

The code release v2 associated with this version of the dataset can be downloaded as a .zip file from the Supplemental Documents section of this page. Future code updates will be accessible from the GitHub repository https://github.com/shu251/V4_tagsequencing_18Sdiversity_q1.