Computer Lab (I)

Introduction of galaxy and UCSC genome browser

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

About galaxy• Galaxy is an open, web-based platform for

data intensive biomedical research.Public server: http://main.g2.bx.psu.edu

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)

Experiment (I): upload Fastq data

Step 1Step 2

Step 3

Step 4

Step 5

Experiment (I)

Experiment (II): FastQC• Get the report of sequencing data quality

Step 1

Step 2

Step 3

Step 4

Step 5

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

Experiment (III): ChIP-seq/MACS

IP-ed DNA

control DNA

Experiment (III): ChIP-seq/MACS

• Many options/parameters– Choose default setting– Check to output wiggle files for IP/control data

Screenshot of results

Save both wiggle files of IP-ed and control DNA

UCSC genome browser

• A web-server to display genome information in graph

• Pre-installed annotation– Gene, repeat, others

• Custom tracks for user upload data

http://genome.ucsc.edu

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

ChIP-seq data in UCSC genome browser

control

IP-ed