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Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

Author(s): Mark Phillip Peterson1, Jacob T Malloy2, Vincent P Buonaccorsi2, James H Marden3

1. Viterbo University 2. Juniata College 3. Pennsylvania State University

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Description

Next-generation sequencing is radically changing the study of biology, but there are currently few resources aimed at teaching the required laboratory and data-analysis skills to undergraduate students. This gap is especially true at primarily undergraduate institutions, where even the faculty are likely to encounter barriers related to funding, equipment, and training needed to begin research or teaching of sequencing and the associated bioinformatics. For this reason, the GCAT-SEEK network has been developed to provide training, data, and teaching materials specifically geared for general biology undergraduates and their instructors. This lesson plan was created to teach RNAseq analysis as a part of that effort.  It is provided here, both in finished form and with the modifiable source code, to allow flexible adaptation to various classroom settings. In addition, we include a relevant tutorial to ease students and faculty into the R statistical environment. The associated materials are directly applicable to both faculty training and classroom settings. We expect implementation of the tutorial to strengthen bioinformatic knowledge and skills for general biology students.

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