Workshop tutorials for the 2017 Benthic Invertebrates, Metagenomics, and Bioinformatics Workshop in Corpus Christi, Tx (January 9-13, 2017)
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README.md

Welcome to the BITMaB workshop - Corpus Christi, TX (January 9-13, 2017)

This workshop provides training on how to describe the taxonomic diversity in a marine benthic community, using both morphological taxonomy and environmental sequencing approaches.

Final workshop Schedule is here: https://docs.google.com/document/d/1H8aHrddJ6VoBwrK6XWA9Zqs5fj8IkqbZIfniPwMKEUQ/edit?usp=sharing

Main Dropbox Folder with all workshop resources is available here: https://www.dropbox.com/sh/p6udtygnk7cf8dr/AAAmpar-QO7jCF_RRxnXigAia?dl=0

Participant List can be found here: https://www.dropbox.com/s/ov3gr2q1k11wl9z/BITMaB_participants_list_2017.pdf?dl=0)

####Sample Info:

Google Map of Workshop Sample Sites: https://drive.google.com/open?id=1PySPGX4VuOVBa2Hq9qdse7c88xU&usp=sharing

QIIME-formatted sample mapping file (Genomic Samples - Ethanol and Zymo Buffer): INSERT LINK


Workshop Schedule (permanent links to talks & handouts)

Monday Jan 9th:

Tuesday Jan 10th:

Wednesday Jan 11th:

Thursday Jan 12th:

Friday Jan 13th:


Getting started

Login using the username assigned to you

ssh username@ron.sr.unh.edu

Setting up a temp directory on Ron

This setup is specific to Ron and may not be needed for other servers.

  • Create a temp directory in your home directory

  • Open your ~/.bashrc in nano

  • Type the following line at the end of your ~/.bashrc and save the file.

export TMPDIR=/home/gomre/USERNAME/temp
  • Source your ~/.bashrc

To use Qiime, run the commands below

enable_qiime.sh
source activate qiime1

Now, you should be in the QIIME environment and ready to run through the pipeline.


Where are all the files?

The locations of all the files you will need for the QIIME tutorial are listed below

Data file - GOM Illumina seqeunces, in fasta format:

/home/gomre/taruna/200k-GOM-Illumina-subsample/data-clean/GOM_concat1.7_subsample200k_10Jan14.fna

Mapping file - tab-delimited spreadsheet containing sample metadata:

/home/gomre/taruna/200k-GOM-Illumina-subsample/qiime-files/mapping-files/QIIMEmappingfile_GOM_Illumina_7Apr14_F04.txt

Parameters file -

/home/gomre/taruna/200k-GOM-Illumina-subsample/qiime-files/parameters/18S_openref99_rdp_silva119.txt

Silva119 database - Publically available reference database files, downloaded from the QIIME website. SILVA is the normal database we use for microbial eukayote metabarcoding analyses (meiofauna, protists, etc.), but other databases you can use include Greengenes (for bacterial/archaeal 16S rRNA data) and UNITE (for fungal ITS rRNA data). Both of these are also available for download at the above QIIME link. Or you can build and use your own custom database!

18S rep set file - unaligned reference sequences, in fasta format

/home/gomre/taruna/200k-GOM-Illumina-subsample/ref-dbs/Silva119_release/rep_set_eukaryotes/99/Silva_119_rep_set99_18S.fna

Aligned 18S rep set fasta - the reference SILVA sequences which were subjected to multiple sequence alignment (using secondary structure information from rRNA)

/home/gomre/taruna/200k-GOM-Illumina-subsample/ref-dbs/Silva119_release/aligned_rep_files/99_18S_only/Silva_119_rep_set99_aligned_18S_only.fna

Taxonomy file - mapping file which links sequence IDs to taxonomic hierarchies (what we usually refer to as "taxonomy strings"")

/home/gomre/taruna/200k-GOM-Illumina-subsample/ref-dbs/Silva119_release/consensus_majority_taxonomy/consensus_taxonomy_eukaryotes/99/taxonomy_99_7_levels_consensus.txt

Full directory of SILVA database files (For reference, in case you want to look around or try out some customized analyses)

/home/gomre/taruna/200k-GOM-Illumina-subsample/ref-dbs/Silva119_release/