1. Computer Lab (I) Introduction of galaxy and UCSC genome browser

2. outlines What’s galaxy How to use galaxy – Upload your data – FastQC – ChIP-seq/MACS How to use UCSC genome browser – Load wiggle/BED files into browser tracks

3. About galaxy Galaxy is an open, web-based platform for data intensive biomedical research. Galaxy Public server: http://main.g2.bx.psu.edu

4. More about galaxy A web-based computing server Many software have been installed You can upload your data to server You can run installed tools to analyze your data You can share your data to others You can also install your own tools (advanced feature)

5. Experiment (I): upload Fastq data Step 1 Step 2 Step 3 Step 4 Step 5

6. Experiment (I)

7. Experiment (II): FastQC Get the report of sequencing data quality Step 1 Step 2 Step 3 Step 4 Step 5

8. Experiment (III): ChIP-seq/MACS You need to at least one dataset: IP-ed DNA It is preferred to have control/input DNA Practise to upload data.bam and control.bam into galaxy

9. Experiment (III): ChIP-seq/MACS IP-ed DNA control DNA

10. Experiment (III): ChIP-seq/MACS Many options/parameters – Choose default setting – Check to output wiggle files for IP/control data

11. Screenshot of results Save both wiggle files of IP-ed and control DNA

12. UCSC genome browser A web-server to display genome information in graph Pre-installed annotation – Gene, repeat, others Custom tracks for user upload data

13. http://genome.ucsc.edu

14. Experiment (IV): show ChIP-seq data in genome browser

15. ChIP-seq data in UCSC genome browser control IP-ed