The MPIC provides histological services, equipment usage, and technical expertise to digestive and liver research projects.
It is funded by the Center for Molecular Studies in Digestive and Liver Diseases (NIH P30 DK050306) and the Program Projects "Mechanisms of Esophageal Carcinogenesis" (P01 CA098101) and "Integrative Metabolic Adaptations to Environmental and Nutritional Challenge" (NIH P01 DK049210).
"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."
"RUM 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."