About RUM
RUM is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.
RUM can also be used effectively for DNA sequencing (e.g. ChIP-Seq) and microarray probe mapping.
RUM also has a strand specific mode.
RUM is highly configurable, however it does not require fussing over options -- the defaults generally give good results.
Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM) Gregory R. Grant, Michael H. Farkas, Angel Pizarro, Nicholas Lahens, Jonathan Schug, Brian Brunk, Christian J. Stoeckert Jr, John B. Hogenesch and Eric A. Pierce.
RUM is freely available to academics and non-profit organizations. However, since RUM uses BLAT, users from industry must first obtain a license for BLAT from the Kent Informatics Website.
RUM is an alignment pipeline that maps reads in three phases. First it maps against the genome using Bowtie, then it maps against a transcriptome database using Bowtie, then it maps against the genome using Blat. The information from the three mappings is merged into one mapping. This leverages the advantages of both genome and transcriptome mapping as well as combining the speed of Bowtie with the sensitivity and flexibility of Blat.
Coverage plots are generated, normalized intensities for genes, introns and exons are generated, and files describing the junctions are generated. Files are also generated that have the alignment for each read, one per line, in RUM and SAM format. These output files are described in more detail in a later section of this user guide.
Please email Gregory Grant with any questions or comments: ggrant@pcbi.upenn.edu.
Gregory R. Grant1,2,4, Michael Farkas3, Angel Pizarro2, Nicholas Lahens5, Jonathan Schug, Brian Brunk1, Christian J. Stoeckert Jr1,4, John B. Hogenesch1,2,5 and Eric A. Pierce3
- Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
- F.M. Kirby Center for Molecular Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
- Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
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