FazalLabPipelines

Viewing Genome Tracks in the UCSC Genome Browser

After running the BamToBigWig pipeline, follow these steps to view your genome tracks in the UCSC Genome Browser.

Go to your processed data folder on the cluster and download every BigWig file that ends in “controls_uns.norm_avg.bw” or “targets_uns.norm_avg.bw” to your local computer.

Note: If you chose to combine controls for data analysis with ProcessCounts, only download one control file: “all_controls_uns.norm_avg.bw”

Note: “uns” stands for unstranded. If you would like to see separate genome tracks for the forward and reverse strands, download the files ending in “controls_fwd.norm_avg.bw”, “controls_rev.norm_avg.bw”, “targets_fwd.norm_avg.bw”, and “targets_rev.norm_avg.bw” instead.
Sign in to BackBlaze (this is the online data hosting service we use in the lab).

Note: The sign in information is in the Lab Passwords document on OneDrive.
Click Browse Files, then select the bucket BigWigFiles.
Add a new folder for your experiment.
Open the new folder and upload your BigWig files.

Open Notepad (Windows) or TextEdit (Mac).
For each BigWig file that you uploaded to BackBlaze: copy and paste this track line on a new line in the blank note, then replace Name and URL.
```
track type=bigWig name="Name" bigDataUrl=URL color=68,68,68 visibility=hide
```
Note: The Name of your track is the name of your BigWig file (but you can remove “.norm_avg.bw” and use spaces instead of underscores if you want).

Note: To get the URL for your BigWig file, click on the file name in BackBlaze to see its details, then copy the “Friendly URL”.
Login to the UCSC Genome Browser (or sign up if you don’t have an account).
Open the custom track management page to add your custom tracks.
Paste your custom track lines into the “Paste URLs or data” text box, then press Submit.

At the top of the screen, select My Data and then Track Collection Builder.
On the right side of the screen next to “Collected Tracks” click Add Collection. Give your collection a name, then click Save.
On the left side of the screen under “Available Tracks”, click the folder labeled “Custom Tracks”. Then click the green plus sign next to each track you just uploaded to add it to your new collection. (You should see the tracks being added under the new collection folder you just made.)
On the right side of the screen, double click each of target tracks and change the color.

Note: Here are some good colors to choose from. Just enter the code into the “Color” box and press Save.
Click GO in the top right corner of the screen to return to the browser.

Scroll down to the collections listed below the viewing window. Make sure that all of the tracks and collections are set to “hide” except for your new collection and the others shown below:
Click configure at the bottom of the viewing window to configure the image according to your preferences. Then click submit.

Note: These are the default settings that I would recommend:
Drag the bar to the left of the GENCODE collection to position the genes above your tracks (as shown below).

Now click the same bar to configure the genes displayed, then click Submit.

Note: These are the default settings that I would recommend:
Click the gray bar to the left of your collection to configure your tracks, then click Submit.

Note: These are the default settings that I would recommend:
If you know of a good gene to have featured when you open your session, type the gene name in the search box and select it from the drop-down list of results.

At the top of the screen, select My Data and then My Sessions.
Under the heading “Save Settings”, locate the option to “Save current settings as named session”. Replace the text hg38 with the name of your session and click submit on the right.

Now anyone can access your session at anytime using the link stored under “My Sessions”.

Happy browsing!