MEDS5420 - UCSC and ChIP-seq peak calling.

Contents

1 Uploading to the browser

You can upload these data (.bed and .bedGraph files) as custom tracks on the browser. Just go to ‘custom tracks’ -> ‘add custom tracks’ and follow instructions.

Uploading Tips:

• Do not reuse track names - they overwrite each other.
  
• It is fastest to upload .gzipped files.
  
• multiple files with tracklines can be concatenated into one file, compressed, and uploaded as a single file.
  

Figure 1: UCSC genome browser

Figure 2: custom tracks view

2 In class exercise 1: Upload data to browser-follow along

Starting with the .bed file and .bedGraph file you just created, do the following.
- Add appropriate track lines to the head of the .bed and .bedGraph files.
- gzip the files
- Transfer from the server to your laptop
- Upload the data onto the UCSC genome browser

3 Using the UCSC genome browser

Switch to PDF slides.

4 In class exercise 2: Using the UCSC genome browser.

1. Find and download the chromosome information file dm6.chrom.sizes for the the drosophila genome version dm6.
2. Use the Table Browser from UCSC to find and download the information for the Genecode genes release 39 (V39) (human genome: hg38). How many items are in the file?
3. Take the lines 50-500 from your .bed file and lift them to the old version of the human genome (hg19). Are all entries found? Does this change the coordinates?
4. Create an image for a screen shot figure from your ATF1 ChIP-seq data. Find a peak and zoom in on a region ~ 5KB +/- your peak. Configure your image as follows:
A. Remove the vertical blue lines from view.
B. Make the text at least size 14 font.
C. Reduce the image width to 540 pixels.
D. Change the track height for the bedgraph to 60 pixels.
E. Arrange tracks such that the bedGraph data is below the .bed data.
F. Hide some unrelated tracks: SNPs, conservation, repeat masker, etc.
G. Attach the track hub from the Roadmap Epigenetics data.
H. View and download the PDF image
5. Share the link with your collaborator (pretend it is me) by saving your session and emailing me a link. Include the .PDF you created in the email.

For answers and hints, see UCSC browser slides

5 Answers to exercises:

5.1 In class exercise 1: upload to browser

1. Use the addTrackLines.sh script we wrote in class to add the track lines.
   
2. Use scp os sftp to copy the files to your computer.
   

I will demonstrate in class.

5.2 In class exercise 2:

For answers and hints, see UCSC browser slides I will demonstrate in class