before we start login to the laptop: user: crgcomu password: crgcomu login to the network: wifi:...

Before we start

•Login to the laptop:• user: crgcomu• Password: crgcomu

•Login to the network:• Wifi: carretwifi• Password : ana@bong

•Login to galaxy (ldap):• User: your web mail user• Password : your web mail password

Galaxy: an Open Web-Based Analysis Platform

Jean-François Taly & Ernesto Lowy

Bioinformatics Unit

CRG (Barcelona, Spain)

Developed by Nekrutenko and others at Penn State, along with James Taylor at Emory University

Galaxy is an open web-based tool for biomedical research

Accessible: users without programming experiencecan easily specify parameters and run tools and workflows

Reproducible: Galaxy captures information so that any user can repeat and understand a complete computationalanalysis

Introduction

Galaxy Interface

Tools

Tool/Data Browser Input Outputhistory

Browsing Data

Running Tool: Bowtie2

28 Public Galaxy Servers

Galaxy Tutorials

Galaxy Workflows

Community Tools

Community Tools

Hardware schema

Galaxy: How to Upload Data?

Jean-François Taly & Ernesto Lowy

Bioinformatics Unit

CRG (Barcelona, Spain)

Galaxy Interface

Tools

Tool/Data Browser Input Outputhistory

Get Data From UCSC

Get Data From UCSC

Get Data From BioMart

Get Data From BioMart

Upload Local Data

Upload Local Data

From your disk

From web server

From ftp server

Upload Data: From Disk

From your disk

Upload Data: File Format

Upload Data: From Disk

Upload Data: Genome

Upload Data: From Disk

Purple = upload is being prepared

Upload Data: From Disk

Yellow = upload is running

Upload Data: From Disk

Green = upload is finished

Browsing Data

Edit Data Attributes

Upload Data: FTP

FTP must be used for big files (>2Gb)

Process in 2 steps:1. Use a FTP client to TEMPORARILY

upload the file into the server2. Use Galaxy to move the file to its

final destination Time before deletion:

◦ In step 1 : 2 weeks◦ In step 2 : Forever

Upload Data: FTP

FTP server name: galaxy.crg.es

Username and Password are the same as the ones of Galaxy!

You need a FTP client:◦Filezilla (all platforms)◦WinSCP (for Windows)◦Fetch (for MAC) ◦gFTP (for Linux)

Upload Data: FTP (Filezilla)

Upload Data: FTP (Filezilla)

Upload Data: FTP (Filezilla)

Do it yourself!

Task:1.Use your prefered FTP client to

upload the file “Human-SE-RNAseq.fastq” in the FTP server

Tip:1.Server name: galaxy.crg.es2.Username & Password: Same as for your CRG mail

Upload Local Data

Upload Local Data

Galaxy: ChipSeq

Jean-François Taly & Ernesto Lowy

Bioinformatics Unit

CRG (Barcelona, Spain)

Chip Seq

Goal of exercice

Input is Chip Seq Reads from◦Specie: mouse, chr19 ◦Cell line: G1E_ER4

Conditions: with or without:◦Transcriptional repressor CTCF

Align reads to the reference genome

Use the treated and control alignments to find peaks

Do it yourself!

Task:1.Use the method you want to upload

the file “G1E_ER4_CTCF_chr9.fastqsanger” in your history

Tip:1.The file is the repertory “experiment1” you should have copied from the pen drive.

2.Do not forget the datatype

Input Data

Quality Check

Quality Check

Running Tool: Bowtie2

Load a file while computing

Do it yourself!

Task:1.Use the method you want to upload

the file “” in your history2.Map the reads to the genome mm9

with bowtie2

Tip:1.The file is the repertory “” you should have copied from the pen drive.

Prepare peak calling (MACS)

Prepare peak calling (MACS)

Check the parameters

Genome Browser: Trackster

Trackster: Create New

Trackster: Create New

Trackster

Trackster: Add track

Trackster: Add track

Workflow

Workflow

Workflow

Workflow

Do it yourself!

Task:1.Use the method you want to upload

the files “G1E_CTCF.fastqsanger” and “G1E_input.fastqsanger” in your history

Tip:1.The file is the repertory “experiment2”

2.Do not forget the datatype3.First the CTCF file and then the control

Workflow

Workflow

Workflow