2014 09 18 TSW at Arthropod Genomics Research in ARS Workshop

Organizers	DeWayne Shoemaker, Monica Poelchau, Chris Childers, Jason Williams
iPlant Trainers	Shabarinath Subramaniam, Jason Williams
Date	September 18-19, 2014
Location	GWCC, Beltsville MD and Online
Designated Lodging:	Sheraton Washington North, Beltsville, MD

ARS Workshop iPlant Talk

iPlant Overview talk presented on 9/17 can be downloaded here.

Pre-Workshop Assignments and prep

Download a packet containing some exercises and recommendations that will prepare you for the workshop

Download: pre-workshop packet

Online Viewing

Virtual attendance is possible via Livestream:

Day I URL:

https://new.livestream.com/cshl-dnalc/ars-day1

(Sep 18th ~12:30-5:30PM EDT)

Day II URL:

https://new.livestream.com/cshl-dnalc/ars-day2

(Sep 19th ~08:00-12:00PM EDT)

Agenda

This agenda is an outline of the activities we will present at the clinic. We will make every effort to make adjustments as needed based upon the needs and interests of the participants.

Download: Handout

The handout contains more topics than will be covered here, but you can work through it with the referenced sample data.

Day 1

Time	Topic	Slides	Links	Presenter(s)
12:30	Overview, goals, and expectations	Slides		Jason
12:35	Managing data in iPlant (up/download, sharing, metadata)	Slides	Data Store Overview YouTube playlist Demo FTP URLs iDrop download	Shabari
01:30	Discovery Environment tutorial - HT Sequence data resources and manipulation (SRA/FastQC/FastX)	Slides	DE Manual FastQC explanations	Jason
02:00	Overview of RNA-Seq and Tuxedo Workflow ARS Sample Data: /iplant/home/shared/iplant_training/ars_workshop/tuxedo_rnaseq	Slides	RNA-Seq protocol paper Honeybee data paper Launch Atmosphere (See pre-workshop packet) ENCODE Rna Standards Nature Biotechnology on RNA-Seq Standards	Shabari
02:30	Break
03:15	Launch Atmosphere instances
03:30	RNA-Seq w/o refference genome (SOAPdenovo-Trans)	Slides	Soapdenovo Trans paper Documentation/website Evaluating RNA-Seq assemblies Histogram tutorial (Atmosphere/R)	Jason
04:00	Introduction to Atmosphere	Slides	Atmosphere Manual YouTube playlist VNC Download	Shabari
05:00 - 5:30PM	Evaluating and visualizing RNA-Seq results (CummeRbund)		CummeRbund documentation Tutorial on cummeRbund (Atmosphere/R)	Jason

Day 2

Time	Topic	Slides	Links	Presenter(s)
08:00	de novo gene assembly and ALLPATHS demo	Slides	ALLPATHS FAQ Assemblethon Additional ALLPATHS slides YouTube playlist	Jason
09:00	Annotating genomes with MAKER		MAKER Tutorial	Shabari
10:00	Break
10:30	MAKER wrapup and discussion on evaluating annotation quality			Shabari/Chris
11:00 - 12:00PM	Annotation and curation with WebApollo	Slides	WebApollo Workshop Examples	Chris/Monica

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