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.  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

4. Galaxy Interface Input Output history

5. Browsing Data

6. Running Tool: Bowtie2

7. 28 Public Galaxy Servers

8. Galaxy Tutorials

9. Galaxy Workflows

10. 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

15. Get Data From UCSC

17. Get Data From BioMart

19. Upload Local Data

20. 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: 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

31. 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)

32. Upload Data: FTP (Filezilla)

35. 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

36. 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 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

41. 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

42. Input Data

43. Quality Check

45. Running Tool: Bowtie2

46. Load a file while computing

47. 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.

48. Prepare peak calling (MACS)

50. Check the parameters

51. Genome Browser: Trackster

52. Trackster: Create New

54. Trackster

55. Trackster: Add track

57. Workflow

61. 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

62. Workflow