ChIP-Seq Analysis – Using CLCGenomics Workbench

1. ChIP-Seq Analysis – Using CLCGenomics Workbench Jan 23,2019 Ansuman Chattopadhyay, PhD Health sciences library system University of pittsburgh ansuman@pitt.edu

2. Topics • Transcription Factor ChIP-Seq • Histone ChIP-Seq • ATAC-Seq

3. Workshop Page https://hsls.libguides.com/chipseq

4. Software @ HSLS MolBio http://hsls.libguides.com/molbio/licensedtools/resources

5. Software registration@ HSLS MolBio https://hsls.pitt.edu/molbio/software_registration

6. Graphical User Interface based software CLC Genomics Workbench Galaxy : http://galaxy.crc.pitt.edu:8080/

7. Partek flow software http://www.partek.com/partek-flow/

8. Taken from Introduction to ChIP-Seq by HPC Tutorial by HBC Training

9. Taken from Introduction to ChIP-Seq by HPC Tutorial by HBC Training

10. Regulatory Elements

11. ChIP-Seq Workflow

13. Taken from Introduction to ChIP-Seq by HPC Tutorial by HBC Training

14. ChIP-Seq Peak Shapes – Narrow and Broad Li etal., Cell 2007.01.015

15. Taken from Introduction to ChIP-Seq by HPC Tutorial by HBC Training

16. Transcription Factor ChIP- Seq

17. Transcription Factor and Histone ChIP-Seq https://www.ncbi.nlm.nih.gov/pubmed/28609469

18. CLCbio Genomics Workbench System Requirements • Windows Vista, Windows 7, Windows 8, Windows 10, Windows Server 2008, or Windows Server 2012 • Mac OS X 10.7 or later. • Linux: Red Hat 5.0 or later. SUSE 10.2 or later. Fedora 6 or later. • 8 GB RAM required • 16 GB RAM recommended • 1024 x 768 display required • 1600 x 1200 display recommended • Intel or AMD CPU required • Minimum 10 GB free disc space in the tmp directory

19. CLC Plugins to Install • Histone ChIP-Seq • Advanced Peak Shape Tools Plugin – Beta Download available at Top Right Corner

20. Center for Research computing (CRC) https://crc.pitt.edu/

21. Request access to CRC https://crc.pitt.edu/apply

22. Connect to CLC Server @ CRC

23. Access to CRC-HTC Cluster – CLC Server If you DO NOT HAVE CRC-HTC account: Use the following for a limited access UserID: hslsmolb PW: library1# Server host: clcbio.crc.pitt.edu Server port: 7777 If you have CRC-HTC account Use – pitt user name; pitt password Server host: clcbio.crc.pitt.edu Server host: 7777

24. You need Secure Remote Access via Pulse to run CLCGx from off campus locations / Pitt Wireless

25. CLC files at the CRC HTC Cluster Reference Sequences Look for Folders organized by PI’s name

26. Create Folders at CRC-HTC

27. 1 Create Folder in SaM-HTC Cluster 2

28. Create Workshop Folder@ CRC 1 2 3

29. TF ChIP-Seq Workflow http://education.knoweng.org/sequenceng/index.html#

30. Taken from Introduction to ChIP-Seq by HPC Tutorial by HBC Training

31. Dataset https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63716

32. GEO Dataset https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63716

33. Download FASTQ ReadsMyoD_Undiff_ChIP-Seq

34. Download FASTQ ReadsMyoD_Undiff_ChIp-Seq

35. ENA : Download FASTQ ReadsMyoD_Undiff_ChIp-Seq

36. Import :FASTQ ReadsMyoD_Undiff_ChIp-Seq 1

37. Import : FASTQ ReadsMyoD_Undiff_ChIp-Seq (single)

38. 1 STEP 1: Import Reads to CLC (Paired End) 2

39. STEP 1: Import Reads to CLC (Paired End) 3 4 5

40. FASTQ format http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217/

41. FASTQ Reads

42. FASTQC Project http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

43. Taken from Introduction to ChIP-Seq by HPC Tutorial by HBC Training

44. Step 2: Create a Seq QC Report 1 2

45. Trim Reads – Adapter Seq etc.

46. Create Adapter List

47. Create Adapter List

48. Create FAST QC Report

49. FASTQC Report

50. Taken from Introduction to ChIP-Seq by HPC Tutorial by HBC Training