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