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Transcript of Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi:...
![Page 1: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/1.jpg)
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
![Page 2: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/2.jpg)
Galaxy: an Open Web-Based Analysis Platform
Jean-François Taly & Ernesto Lowy
Bioinformatics Unit
CRG (Barcelona, Spain)
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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
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Galaxy Interface
Tools
Tool/Data Browser Input Outputhistory
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Browsing Data
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Running Tool: Bowtie2
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28 Public Galaxy Servers
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Galaxy Tutorials
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Galaxy Workflows
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Community Tools
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Community Tools
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Hardware schema
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Galaxy: How to Upload Data?
Jean-François Taly & Ernesto Lowy
Bioinformatics Unit
CRG (Barcelona, Spain)
![Page 14: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/14.jpg)
Galaxy Interface
Tools
Tool/Data Browser Input Outputhistory
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Get Data From UCSC
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Get Data From UCSC
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Get Data From BioMart
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Get Data From BioMart
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Upload Local Data
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Upload Local Data
From your disk
From web server
From ftp server
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Upload Data: From Disk
From your disk
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Upload Data: File Format
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Upload Data: From Disk
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Upload Data: Genome
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Upload Data: From Disk
Purple = upload is being prepared
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Upload Data: From Disk
Yellow = upload is running
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Upload Data: From Disk
Green = upload is finished
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Browsing Data
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Edit Data Attributes
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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
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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)
![Page 32: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/32.jpg)
Upload Data: FTP (Filezilla)
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Upload Data: FTP (Filezilla)
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Upload Data: FTP (Filezilla)
![Page 35: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/35.jpg)
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
![Page 36: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/36.jpg)
Upload Local Data
![Page 37: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/37.jpg)
Upload Local Data
![Page 38: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/38.jpg)
Galaxy: ChipSeq
Jean-François Taly & Ernesto Lowy
Bioinformatics Unit
CRG (Barcelona, Spain)
![Page 39: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/39.jpg)
Chip Seq
![Page 40: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/40.jpg)
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
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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
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Input Data
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Quality Check
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Quality Check
![Page 45: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/45.jpg)
Running Tool: Bowtie2
![Page 46: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/46.jpg)
Load a file while computing
![Page 47: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/47.jpg)
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.
![Page 48: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/48.jpg)
Prepare peak calling (MACS)
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Prepare peak calling (MACS)
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Check the parameters
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Genome Browser: Trackster
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Trackster: Create New
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Trackster: Create New
![Page 54: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/54.jpg)
Trackster
![Page 55: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/55.jpg)
Trackster: Add track
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Trackster: Add track
![Page 57: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/57.jpg)
Workflow
![Page 58: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/58.jpg)
Workflow
![Page 59: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/59.jpg)
Workflow
![Page 60: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/60.jpg)
Workflow
![Page 61: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/61.jpg)
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
![Page 62: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/62.jpg)
Workflow
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Workflow
![Page 64: Before we start Login to the laptop: user: crgcomu Password: crgcomu Login to the network: Wifi: carretwifi Password : ana@bong Login to galaxy (ldap):](https://reader037.fdocuments.in/reader037/viewer/2022102805/551b9428550346d6338b607d/html5/thumbnails/64.jpg)
Workflow