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Before we start

Before we start. Login to the laptop : user: crgcomu Pass word: 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.

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Before we start

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  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): • User: your web mail user • Password : your web mail password

  2. Galaxy: an Open Web-Based Analysis Platform Jean-François Taly & Ernesto Lowy Bioinformatics Unit CRG (Barcelona, Spain)

  3. 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

  4. Galaxy Interface Input Output history Tools Tool/Data Browser

  5. Browsing Data

  6. Running Tool: Bowtie2

  7. 28 Public Galaxy Servers

  8. Galaxy Tutorials

  9. Galaxy Workflows

  10. Community Tools

  11. Community Tools

  12. Hardware schema

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

  14. Galaxy Interface Input Output history Tools Tool/Data Browser

  15. Get DataFrom UCSC

  16. Get Data From UCSC

  17. Get Data From BioMart

  18. Get Data From BioMart

  19. Upload Local Data

  20. Upload Local Data From your disk From web server From ftp server

  21. Upload Data: From Disk From your disk

  22. Upload Data: File Format

  23. Upload Data: From Disk

  24. Upload Data: Genome

  25. Upload Data: From Disk Purple = upload is being prepared

  26. Upload Data: From Disk Yellow = upload is running

  27. Upload Data: From Disk Green = upload is finished

  28. Browsing Data

  29. Edit Data Attributes

  30. Upload Data: FTP • FTP must be used for big files (>2Gb) • Process in 2 steps: • Use a FTP client to TEMPORARILY upload the file into the server • Use Galaxy to move the file to its final destination • Time before deletion: • In step 1 : 2 weeks • In step 2 : Forever

  31. Upload Data: FTP • FTP server name: galaxy.crg.es • Username and Password are thesame as theones of Galaxy! • Youneed a FTP client: • Filezilla (allplatforms) • WinSCP (for Windows) • Fetch (for MAC) • gFTP (for Linux)

  32. Upload Data: FTP (Filezilla)

  33. Upload Data: FTP (Filezilla)

  34. Upload Data: FTP (Filezilla)

  35. Do it yourself! • Task: • Use yourprefered FTP clienttouploadthefile “Human-SE-RNAseq.fastq” in the FTP server • Tip: • Server name: galaxy.crg.es • Username& Password: Same as foryour CRG mail

  36. Upload Local Data

  37. Upload Local Data

  38. Galaxy: ChipSeq Jean-François Taly & Ernesto Lowy Bioinformatics Unit CRG (Barcelona, Spain)

  39. Chip Seq

  40. Goal of exercice • Input is Chip SeqReadsfrom • Specie: mouse, chr19 • Cell line: G1E_ER4 • Conditions:withorwithout: • TranscriptionalrepressorCTCF • Alignreadstothereferencegenome • Use thetreated and control alignmentstofindpeaks

  41. Do it yourself! • Task: • Use themethodyouwanttouploadthefile “G1E_ER4_CTCF_chr9.fastqsanger” in yourhistory • Tip: • Thefileistherepertory“experiment1” youshouldhavecopiedfromthepen drive. • Do notforgetthedatatype

  42. Input Data

  43. Quality Check

  44. Quality Check

  45. Running Tool: Bowtie2

  46. Load a file while computing

  47. Do it yourself! • Task: • Use themethodyouwanttouploadthefile “” in yourhistory • Mapthereadstothegenome mm9 with bowtie2 • Tip: • Thefileistherepertory “” youshouldhavecopiedfromthepen drive.

  48. Prepare peak calling (MACS)

  49. Prepare peak calling (MACS)

  50. Check the parameters

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