Galaxy-BasicTraining - Bioinformatics Core at CRG

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Before we start
•Login
to the laptop:
•user: crgcomu
•Password: crgcomu
•Login
to the network:
•Wifi: carretwifi
•Password : [email protected]
•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)
Introduction
 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
Galaxy Interface
Input
Output
history
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
Input
Output
history
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 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)
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.es
2.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 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)
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 datatype
3.First the CTCF file and then the control
Workflow
Workflow
Workflow

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