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Trinotate and TrinotateWeb demo on iPlant atmoshpere

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt/Uniref90), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (singalP/tmHMM), and comparison to currently curated annotation databases (EMBL Uniprot eggNOG/GO Pathways databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.

If you don't have an iPlant account: You can register for your account at https://user.iplantcollaborative.org/register/. After registering, go to https://user.iplantcollaborative.org/dashboard/ to request access to the Atmosphere service by clicking on 'Request Access'.

Running Trinotate on iPlant Atmosphere

  1. Launch instance -- Log in to atomsphre-> Click on "Launch New Instance" -> Type in search "Trinotate_RNAseq_annotation_v2" and select -> Select image size & Click on Launch Instance
  2. Connect to instance -- You can either ssh thorugh terminal of using UNIX or Mac machine or using putty on windows or connecting to the instance via VNC

ssh username@<IP_Address_of_instance>

  1. Download Trinoate with example data --

wget --no-check-certificate https://de.iplantcollaborative.org/dl/d/ED99CD7F-BAE9-48D5-B74E-E012AB465401/Trinotate-2.0.2.tar .

tar -xvf Trinotate-2.0.2.tar

  1. Run test runMe.sh script --

Change directory to sample data

`cd Trinotate-2.0.2/sample_data`

`sh runMe.sh`

This will run the entire Trinotate pipeline sequentially. 5. Output -- Look for the following files

Trinotate_report.xls- annotations file

myTrinotate.sqlite-Trinotate sqlite database file

Running TrinotateWeb on iPlant Atmosphere

  1. ** Connect to instance via VNC viewer**-- Use VNC Viewer to connect to instance
  2. ** Open Terminal**--

cd ../TrinotateWeb

sh run_mongoose_webserver.sh

This will start the mongoose web server

  1. Open chrome web browser-- go to your web browser and paste the URL:

http://localhost:8080/cgi-bin/index.cgi

You should be prompted to enter in the path to your Trinotate sqlite database.

  1. Enter the path for Trinotate sqlite database

/home/<iplant_username>/Trinotate-2.0.2/sample_data/myTrinotate.sqlite

Trinotate reference