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The PMM Bioinformatics Core has the capability for data analysis, workflow/pipeline/package development and consultation.

Data Analysis and Workflow Development

The PMM Bioinformatics Core capability includes the following areas:

(1) Analyzing data generated from next-generation sequencing (NGS) for RNASeq, small RNA-Seq, single-cell RNASeq, ExomeSeq, ChIPSeq, ATAC-Seq, chRNA-seq, iCLIP, and 3’ end Sequencing. NGS analyses include pre-alignment QC, alignments, post-alignment QC, quantification and function enrichment analysis and results interpretation.

(2) Apply of existing Bioinformatics packages and toolkits to develop automation pipelines that can be used in either dolphinnext or MGHPCC directly. To use pipelines specifically designed for PMM users, please contact us.

(3) Bioinformatic package development for a novel or specifically designed sequencing technology, and analytic procedure that doesn’t mature package available (e.g., APAlyzer for APA analysis using RNA-seq)

(4) Customized downstream analysis. Not only to construct the expression, splicing, polyadenylation, RBP binding, and histone modification profiles and gene set clusters but also to capture genomic and transcriptomic features such as sequence motifs, mutations, splicing score, intron size, target and binding sites involved in the regulatory mechanism for transcriptional, medical and clinical research.

(5) Genomic resource development and database construction. Identify and develop genome-wide resource for target species, and build the corresponding database and website to maintain  (e.g., PolyA_DB3 for polyA sites identified from vertebrates)

(6) De novo/mapping whole genome assembly, annotation, high-density linkage map construction for non-model species without available genome. (e.g., sea cucumber whole genome)

Bioinformatics Consultation

(1) Grant Proposal Assistance. A comprehensive plan and suitable expertise for data analysis, management and visualizations can spell “SUCCESS” for grant proposals. The Core can assist with experimental design, budget planning (for required IT equipment, software licenses and effort from Bioinformatics personnel), and facilities statements and provision of letters of support. In addition, the Bioinformatics Core members can be project participants (Co-PI, Co-Investigator, Collaborator) providing an additional level of expertise to a research proposal.

(2) Experimental and analysis design. The core offers consultation on a range of Bioinformatics topics, from project design to data analysis. Co-ordinated consultation services for project design of projects with other Cores or departments is available (for example Deep Sequencing Core or the Quantitative Health Sciences Department). It is best to engage in experimental design consultations before the experiments are carried out.

(3) Various types of troubleshooting. If you want to carry out your own bioinformatics analysis but have questions along the way. The Core can help troubleshoot as needed.