2014 11 10 Train-the-trainers Webinar

Video Recording

The video for this event is now posted: http://youtu.be/B3jsGNuoF-k

Workshop Checklist

1. iPlant Account

• Get your free account at http://user.iplantcollaborative.org.

2. Atmosphere Access

• Once you have your account, go to https://user.iplantcollaborative.org/dashboard/ and under Available Services, request access  to Atmosphere. Indicate that you are attending a workshop when you are asked for justification.

3. Uploaded Data (Optional)

If you are bringing data to the workshop, please follow the instructions below. It is recommended to upload your data before attending the workshop. You should upload from the best possible internet connection, and if you have any issues email support@iplantcollaborative.

Depending on your level of comfort and the size of the data, you may want to try one of two methods.

1)   iDrop – a desktop drag/drop utility

2)   iCommands – command line interface 

For iDrop, you can-http://bit.ly/1i7wm4s- follow the instructions for downloading and configuring iDrop here

• You can read documentation here: bit.ly/PuWXPP
• You can see a video explanation here: http://youtu.be/0YiMG3OMbhM

For iCommands, you can download the scripts here: bit.ly/1kNdDyR

• You can read documentation here: bit.ly/1frB8W1
• You can see a video explanation here: http://youtu.be/C8tLzBdNG8Y

When uploading via iCommands (using iput) it is recommended that you use the T option to renew the connection socket, especially for single large (>30GB) files. The documentation also discusses the options to display progress and to create a restart file. 

Once you have uploaded the data, please fill out this survey (https://docs.google.com/forms/d/1DdQMjk_ri9L4eEma5AOLiRsGMOPRwOB0mVezThF_W2o/viewform ) so that we can have a clearer idea of what data you will be bringing.

4. Laptop

You must bring your own WiFi enabled laptop to the workshop. Please be sure your laptop has the following:

• VNC Viewer: Download the DMG (for MAC) or exe (for PC): http://www.realvnc.com/download/viewer/
• Java: Please have JAVA installed and enabled (help)
• Browser: Please have an up-to-date web browser (Recommended Firefox or Safari )

Notes and Help

Here are a few important links that you may wish to refer to during and after the workshop:

Account/Password Problems

• user.iplantcollaborative.org

iPlant Help and Discussion Forums

• forums.iplantcollaborative.org/
• http://ask.iplantcollaborative.org

General iPlant Support Issues

• support@iplantcollaborative.org

iPlant Privacy (And other) policies - "Your Data is Your Data"

• www.iplantcollaborative.org/privacy
• www.iplantcollaborative.org/about/data-set-hosting
• www.iplantcollaborative.org/about/general-usage-policy

Background reading

• Transcriptome assembly principles- Transcriptome_assembly_principles.pdf
• Trinity tool-Trinity_assembly_tool.pdf
• Trinity downstream analysis- Trinity_downstream_analysis.pdf
• Screen cast videos- Brian Haas- Trinity Developer- Broad Institute- http://www.broadinstitute.org/partnerships/education/broade/trinity-screencast

• • Trinity Tutorial: ftp://ftp.broadinstitute.org/pub/users/bhaas/rnaseq_workshop/rnaseq_workshop_2014/Trinity_workshop_activities.pdf
  • Tuxedo Tutorial: ftp://ftp.broadinstitute.org/pub/users/bhaas/rnaseq_workshop/rnaseq_workshop_2014/Tuxedo_workshop_activities.pdf

• Refernce Guided trinity assembly-using Tuxedo protocol- Tuxedo_paper.pdf
• SOAPdenovo-Trans-SOAPdenvo-Trans.pdf

Protocols

Updated protocols for your analysis

Action Items

• After the call: Arrange for a group introduction - email, Skype, Google hangout, etc.
• Depending on the call results we want all teams to have access to a dataset by Wednesday (Nov. 12th)
• By Nov. 12th we will have posted some more details to the protocols above, but essentially the goal is for the team to process and start the assembly asap.
• There will be decision points along the way (e.g. how to trim and normalize) each team will have to communicate, and Jason and Kapeel are also available for help.

Teams for the December Workshop