The study identified strengths and weaknesses in research governance at the University of Ghana (UG) with respect to the organization of research, Institutional Steering of Research and the management of research. It presents issues, capacity building requirements, and recommendations to the government of Ghana, the University of Ghana, research funders and researchers. It recommends the government of Ghana put in place a National Research Policy and provide improved infrastructure to promote research governance at UG. Capacity building requirements include training in research project management and administration, fund raising and proposal writing, dissemination of results, and strategic planning

Chesnokov M.

Kasianov A.

Klepikova A.

Lazarevich N.

Logacheva M.

Penin A.

© 2017 Klepikova et al.Background. RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. Results. To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in samtools, and deduplication based on one or two molecular indices (MI).Wealso analyzed the influence of sequencing layout (single read or paired end) and read length. We found that deduplication without MI greatly affects estimated expression values; this effect is the most pronounced for highly expressed genes. Conclusion. The use of unique molecular identifiers greatly improves accuracy of RNA-seq analysis, especially for highly expressed genes. We developed a set of scripts that enable handling of MI and their incorporation into RNA-seq analysis pipelines. Deduplication without MI affects results of differential gene expression analysis, producing a high proportion of false negative results. The absence of duplicate read removal is biased towards false positives. In those cases where using MI is not possible, we recommend using paired-end sequencing layout

National Open Repository Aggregator (NORA)

Effect of method of deduplication on estimation of differential gene expression using RNA-seq

Tobbin, Mary

International Development Research Centre: IDRC Digital Library