Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : 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 experience can easily specify parameters and run tools and workflows  Reproducible: Galaxy captures information so that any user can repeat and understand a complete computational analysis Introduction

Galaxy Interface Input Output history

Browsing Data

Running Tool: Bowtie2

28 Public Galaxy Servers

Galaxy Tutorials

Galaxy Workflows

Community Tools

Hardware schema

Galaxy: How to Upload Data? Jean-François Taly & Ernesto Lowy Bioinformatics Unit CRG (Barcelona, Spain)

Galaxy Interface Input Output history

Get Data From UCSC

Get Data From BioMart

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 server 2.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)

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.es 2.Username & Password: Same as for your CRG mail

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

Running Tool: Bowtie2

Load a file while computing

Do it yourself! Task: 1.Use the method you want to upload the file “” in your history 2.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)

Check the parameters

Genome Browser: Trackster

Trackster: Create New

Trackster

Trackster: Add track

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 datatype 3.First the CTCF file and then the control

Workflow