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Viewing Output

There are two choices for viewing the output from SpliceMap; UCSC Genome Browser or cisGenome Browser. These instructions will be expanded on in the future. Please contact us if you have any concerns.

UCSC Genome Browser

Viewing the output in UCSC Genome browser is simple, the output is already formatted so that it can be readily accepted by the browser. However, due to the large size of coverage files, you may have to host them locally with cisGenome Browser.

cisGenome Browser

cisGenome Browser is a light-weight alternative to UCSC browser. It is run on your own personal computer.

The junction .bed files are directly readable by cisGenome browser. The coverage .wig files need to be converted to .bar with the following steps. For instance, if you wanted to convert the file coverage.wig:

  1. Run "wig2bigwig coverage.wig coverage.barwig"
  2. Run "barloader coverage.barwig"
  3. The resulting file "coverage.barwig.bar" can be read by cisGenome Browser

"barloader" has a high memory requirement, for 36 million reads on the mouse genome you will need over 20G of RAM.

The following is some example output from cisGenome Browser