This documentation is intended for both researchers and bioinformaticians and comprehensively describes the Bioinformatics Shared Resource (BISR). Our goal at the BISR is to enable data-drive insights with quick turnaround times. For researchers we highly recommend and ask you to carefully read our For Research Collaborators section. For bioinformaticians the For Bioinformatics Pipelines sections will be most relevant and non-BISR bioinformaticians are welcome to utilize our pipelines. Lastly, the For BISR Logistics section is for internal matters specific to VCU operations.
As users of the BISR, we want you to understand what we can deliver and the requirements/expectations we have in order to generate speedy and accurate results. In order to understand these requirements we have the following subsections:
- Collaborating with Us - Description of our expectations, our BISR workflow, and frequently asked questions
- Preparing a Samplesheet - Instructions for the generation of a samplesheet (where applicable)
- Overview of the RNA-seq Pipeline - High-level overview of our RNA-seq pipeline with a manuscript ready paragraph
- Common Downstream Analyses - Description of common downstream analyses we perform following our automated pipeline analyses
- Specialized/Custom Work - Explanation of specialized work that is currently outside of our automated pipelines/immediate expertise
To generate consistent and quick results we have setup several community developed pipelines from nextflow. In addition, we have implemented custom pipelines where required. This section includes step-by-step guides for all of these pipelines and contributes to the overall transparency of our code base. Briefly, the corresponding subsections include:
- The Bioinformatics Rundown - Introduction of bioinformatics resources used by the BISR
- Technical & nextflow Overview - Description of nextflow and its use within the VCU servers
- RNA-seq Step-by-Step Guide - Detailed usage guide for RNA-seq data
- Developing a New Core Pipeline - Explaining the process of introducing new pipeline into the BISR workflow
- Pushing Custom Code to Github For Publications - Explaining how to upload publication ready code
To generate consistent and quick results we have setup several community developed pipelines from nextflow. In addition, we have implemented custom pipelines where required. This section includes step-by-step guides for all of these pipelines and contributes to the overall transparency of our code base. Briefly, the corresponding subsections include:
- Managing Projects and Time Tracking on Jira - Rundown of using Jira for both internal and external projects with helpful tips & tricks for time tracking
- Deciding Between Using Athena or Apollo - Description of differences between Athena and Apollo and when to use one versus another
- Understanding Key Storage Drives & Folders - Layout of the different storage drive and folders for past and current BISR projects/results