Custom tracks in the UCSC Genome Browser

I put up a custom track on the UCSC genome browser for the BWA alignment of a small portion of the reads from INTACT DNA run YAS11_CGATGT_L006_R1_001 for chr2L. I wanted to let everyone take a look at it and see if you want more tracks.

Here's how to view the track. 

Point your browser to https://genome.ucsc.edu/cgi-bin/hgCustom

Select the insect clade, the D. melanogaster genome and the Apr 2006 assembly

Copy the following text and paste it into the text box:

track type=bam name="INTACT DNA YAS11" bigDataUrl=http://ccmbweb.ccv.brown.edu/bam/YAS11_CGATGT_L006_R1_001/chr2L.extract-sorted.bam

You should see something like this

Click the submit button. You should see something like 

Click go to genome browser

The genome browser may not take you to chr2L or it may take you to a region without reads. Paste chr2L:826,001-851,000 into the location box.

You should see something like the following, but the details will vary depending on the options you selected the last time you used the browser.

Notice the first track, INTACT DNA YAS11. Clicking on it will expand the track.

You will see something like:

The lines are collections of reads. This is too dense to select any reads, so zoom in. Press the 10X zoom in button at the top twice or until you can click on a single read.

Click on one of the boxes. You should get details of the mapping of that read.

Go back to the browser, and you can view the mapping at your favorite gene in this region.