HOMER

Software for motif discovery and next-gen sequencing analysis

Primary Research Data

UCSC Genome Browser visualization files

1. Pay attention to the GENOME VERSION.  Researchers are constantly trying to improve reference genomes, and when a new version comes out the absolute position of everything changes.  If you upload these files to the wrong version, sometimes it will complain because certain chromosomes or random fragments do not exist.  If you get this error make sure the version is correct.  Sometimes it won't complain, which is worse since all of the peaks etc. will be in the wrong positions.
   
2. DO NOT UNZIP these files when uploading them.  UCSC takes zipped files, and if you try to upload an unzipped version you'll find it's harder to get it to successfully load.
3. If you're having trouble loading them, try "right-clicking" on the links below and "Copy Link Location".  You can past this in to the field when loading custom tracks - this way UCSC will directly load the file from the biowhat.ucsd.edu server instead of from your computer.
4. Don't like my ugly colors for some of the tracks?  Colors for each experiment were generated randomly, and if you don't like them, or they are hard to see, or you want to stick to a different color coding scheme, click on the "manage custom tracks" button and then click directly on the name of the track.  This will give you access to the configuration data for the track.  There will be a part of the text box with "color=r,g,b" that you can directly modify to get the color you want.
   

Notes on Homer UCSC files

Data from the Glass Lab

Data from the Murre Lab

Lymphocyte Inputs

Data from the Katzenellenbogen Lab