Bioinformatics
GTAC@MGI, as a group, has a long track record of developing pipelines and computational tools for enabling biomedical research. We provide a variety of analysis pipelines to help investigators process and understand their sequence data, essentially, performing the computationally intense analysis steps on a cluster or server to produce data and results that can be viewed on a desktop computer. Standard deliverable files provided for different analytical pipelines are noted below.
COMPBIO
COMPBIO (COmprehensive Multi-omics Platform for Biological InterpretatiOn) is a biological knowledge generation platform designed and invented at the Genome Technology Access Center (GTAC) at WashU. The platform can analyze single or multi-omic data entities (genes, proteins, microbes, metabolites, miRNA) and deliver a holistic, contextual map of the core biological concepts and themes associated with those entities. COMPBIO assembles these maps employing contextual language processing algorithms to scan all of Pubmed abstracts (and soon full-text articles) to identify enriched concepts associated with the entities utilizing an ontology-free approach. This novel method allows for rapid identification of unique insights that are otherwise not achievable with existing bioinformatic pathway and ontology analysis tools. The presentation of the results in the custom visualization interface enables knowledge assimilation in an unprecedented fashion.
Availability
Web-based, free to all WashU investigators and their labs. Request your lab account via COMPBIO.
Local Contact
If you have any questions about COMPBIO, please contact the COMPBIO team at GTAC@MGI at gtac-compbio@email.wustl.edu or Marcy Vana at Becker Library at vanam@wustl.edu.
GTAC@MGI, as a group, has a long track record of developing pipelines and computational tools for enabling biomedical research. We provide a variety of analysis pipelines to help investigators process and understand their sequence data, essentially, performing the computationally intense analysis steps on a cluster or server to produce data and results that can be viewed on a desktop computer. Standard deliverable files provided for different analytical pipelines are noted below.
Sequencing Pipelines
- RNA-Seq-FASTQ files, BAM files, count tables, differentially expressed genes
- Whole Genome Sequencing-FASTQ files, BAM files, VCF files, annotated variant files, some filtering of variants
- Exome and Targeted Sequencing-FASTQ files, BAM files, VCF files, annotated variant files, some filtering of variants
- Somatic Variant T/N-FASTQ files, BAM files, VCF files, annotated variant files, some filtering of variants
- 16S analysis using MVRSION-FASTQ files, BAM files, QIIME tables and graphs
- ChIP-seq with the ENCODE pipeline-FASTQ files, BAM files, ChIP-peaks, annotated peaks, data displayed in WU Epigenom Browser
Single Cell Analysis
- SMRT-seq (FACS-seq)- FASTQ files, BAM files, count tables, cell clusters, differentially expressed genes
- 10x Cell Ranger scRNA-seq– FASTQ files, Cell Ranger output: BAM files, matrix files
- 10x Cell Ranger ATAC-seq– FASTQ files, Cell ranger ATAC output: BAM files, matrix files
- 10x Cell Ranger Feature Barcodes– FASTQ files, Cell Ranger output: BAM files, matrix files
- 10x Cell RangerVDJ analysis– FASTQ files, Cell Ranger output: BAM files
- 10x Cell Ranger Multiomic analysis– FASTQ files, Cell Ranger ARC output: BAM files