ENCODE RNA Dashboard

HUB5 - Heidelberg21. March 2013

Maik RöderPython Consultantroeder@berg.net

http://genome.crg.es/encode_RNA_dashboard

Thursday, March 21, 13

ENCODE RNA Dashboard• The ENCODE project has produced

massive amount of transcriptome data

• How to keep up to date during production, even before submission to the ENCODE Data Coordination Center (DCC)?

• Direct links to additional summary statistics produced by the Grape RNA-Seq pipeline

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USCS Genome Browser - ENCODE

• First, a look at the current UCSC genome browser Experiment Matrix for ENCODE

• http://genome.ucsc.edu/ENCODE/

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ENCODE Experiment Matrix (UCSC)

RNA-Seq

Files

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Search + List (UCSC)

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Mouse Experiment Matrix (UCSC)

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Search + List (UCSC)

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ENCODERNA dashboard

• http://genome.crg.es/encode_RNA_dashboard/hg19/

• Summary of transcriptome data production

• Overview

• Exploration

• Batch Download

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ENCODE RNA DashboardHuman (hg19)

Exploration

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ExplorationClick to make file details appear in

place

Click again to make list disappear and continue exploring

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ENCODE RNA Dashboard Mouse (mm9)

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Exploration

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Batch Download• http://genome.crg.es/

encode_RNA_dashboard/HOWTO_batch-download.html

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Today• ENCODE dashboard still remains the only

central place collecting all the RNA data produced by the ENCODE project

• The international research community can explore the wide range of experiments

• Quickly find and download the exact data sets they need for their own data analysis.

• command line users will enjoy the friendly batch processing capabilities

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Upcoming

• Dashboard generation tool

• Reimplementation in Python using Pandas

• Methods Paper to be published soon

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Thanks• This work has been supported by the Centre for

Genomic Regulation (CRG) in Barcelona

• Roderic Guigó

• Julien Lagarde

• Learn about Pandas at the Python Meetup:

• Monday, April 15th

• http://www.meetup.com/HeidelbergPython

Thursday, March 21, 13