RUM is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. It can be used effectively for DNA sequencing (e.g. ChIP-Seq) and microarray probe mapping, and has a strand specific mode. RUM is highly configurable, however it does not require fussing over options -- the defaults generally give good results.

Resources

• On-line documentation.

Users may direct questions to sys-help@loni.org.