Functional Genomics

• Chromatin Structure Analysis
• Workflow Walkthrough
• Results Walkthrough
• Epigenomics: DNA Methylation Detection
• Workflow Walkthrough
• Results Walkthrough
• Optimize a Nucleotide Sequence
• Workflow Walkthrough
• Results Walkthrough
• Expression Analysis in RNASeq
• Workflow Walkthrough
• Results Walkthrough
• Single-Cell Analysis
• Workflow Walkthrough
• Results Walkthrough
• Genomic Variant Analysis
• Workflow Walkthrough
• Results Walkthrough

Chromatin Structure Analysis

Workflow Walkthrough

1. Navigate to the Chromatin Structure Analysis workflow. You can use the search tool at the top-right corner or find the launch card using the “Functional Genomics” or “Next-Generation Sequencing” filters.
2. Select version 1.0.2 from the dropdown menu in the top right corner

3. Click “Run Workflow” in the top right corner
4. Launcher Tabs
1. First, choose the analysis you wish to perform - currently, we support CHIPSeq, ATAC-Seq, STARR-Seq, Cut and Run, and Cut and Tag. Next, select a reference genome. Last, provide the directory of files for analysis and a NGS sample attributes file relating run ID to sample IDs.

2. Edit parameters for the workflow run - these choices may look different depending on what analysis you are performing.

3. Give your workflow a unique name, and review the input files and parameters set for your workflow. When satisfied, click “Run Workflow” to begin your analysis.

Results Walkthrough

1. Locate your workflow from the Activity tab and select it.
2. Once inside, select the Files tab. In this tab, select the output folder. Within this folder you can view HTML reports for your analysis.

Epigenomics: DNA Methylation Detection

Workflow Walkthrough

1. Navigate to the Epigenomics: DNA Methylation Detection launcher card. You can use the search bar at the top right corner or use the Functional Genomics or Next Generation Sequencing tags to find the workflow card.

2. Select version 0.0.3 from the dropdown menu. When ready to begin analysis, select “Run Workflow” at the top-right corner.

3. This workflow currently supports two analysis functions: Reduced Representation Bisulfite Sequencing with Bismark, and Oxford Nanopore Technology analysis with Deepsignal2. Select the analysis you wish to run from the dropdown menu. We’ll choose Bismark.

4. Upload the sequencing files for analysis by clicking the “Select Directory” button.

5. Upload a sample attributes file to help with analysis.

6. Select a reference genome from the dropdown menu.

7. Give your workflow run a unique name, and review the inputs and parameters for the workflow. When you’re satisfied, press “Run Workflow” to begin analysis.

Results Walkthrough

1. Select your workflow from the Activity tab.
2. In this tab, select the Files tab to view all file outputs. You may also view these files in the pipeline-outputs tab of the File Explorer.

Optimize a Nucleotide Sequence

Workflow Walkthrough

1. Navigate to the Optimize a Nucleotide Sequence workflow
2. Select version 1.0.2 from the dropdown menu

3. Click “Run Workflow”
4. Launcher Tabs
1. Provide sequence name and raw sequence or files corresponding to the sequence

2. Review workflow parameters and name workflow run

3. Click “Run Workflow”

Results Walkthrough

1. To view results, first locate your run in the Activity tab. Once found, select it to view more information. On this page, you can view information about the workflow status, analysis outputs, files input and output, parameters, and Nextflow logs.

2. Select Analysis from the tabs to view the results of the workflow run. You may also click View Full Screen Results to open the results in a new tab.

Expression Analysis in RNASeq

Workflow Walkthrough

1. Navigate to the Expression Analysis in RNASeq launcher card. You can use the search bar at the top right corner, or use the Precision Medicine, Functional Genomics, or Next Generation Sequencing tags to find the workflow card.

2. Select version 1.0.0 from the dropdown box in the top right corner. WHen ready to begin analysis, click “Run Workflow”.

3. This workflow currently supports four analysis functions: Expression Detection, Recalculate Statistics, Compare Alignments, and Human Cancer. Let’s look at the Recalculate Statistics options, for repeating statistical analysis performed in previous workflow runs. Select this function from the dropdown box.

4. Select a reference genome and annotation version for the workflow run.

5. Name the workflow run, then take a minute to review workflow settings and parameters. When you’re satisfied, click “Run Workflow” at the bottom-left corner.

Results Walkthrough

1. To view results for your Expression Analysis in RNASeq workflow, first find your workflow run from the Activity tab of the platform. Select your workflow run for more information.

2. After selecting your workflow run, you may click Open Analysis to view an interactive summary of the RNASeq analysis. You may also navigate the the Files tab and view and download analysis outputs in the output folder. These folders are also available in the File Explorer.

3. Navigate the RNASeq Analysis portal to view specific slices of your analysis.

Single-Cell Analysis

Workflow Walkthrough

1. Navigate to the Single-Cell Analysis workflow launcher. You can use the search bar at the top right to navigate this workflow or you can use the Functional Genomics or Next-Generation Sequencing filters on the left-hand side.
2. Select version 0.1.0 from the dropdown versioning menu. You can view information about the use-cases and workflow analysis here. When ready to begin, click Run Workflow.

3. Select your data input type, either CellRanger output, Illumina, or FastQ files. Then, provide matrix, barcodes, and genes files.

4. Select the host genome, used to help determine contaminants

5. Give your workflow run a unique name, then review input data and parameters. When ready to submit, click Run Workflow.

Results Walkthrough

1. To view results of your Single-Cell Seq workflow, find your workflow run on the Activity tab and then select your run for more information.
2. In this view, select the Analysis tab to view a summary of your workflow analysis. You may opt to view this workflow in a new tab as well.

3. Alternatively, select the Files tab and navigate to the output folder to view or download the HTML results report.

Genomic Variant Analysis

Workflow Walkthrough

1. Navigate to the Genomic Variant Analysis workflow launcher on the Form Bio platform. You can locate the workflow using the search bar at the top right corner, or by using the Precision Medicine or Next-Generation Sequencing filters on the left-hand side.
2. Select version 1.2.0 from the dropdown versioning menu in the top right corner. On this page, you can find information about the workflow analysis. When ready to begin, click Run Workflow.

3. Select the type of input data to be analyzed. Currently, four types are supported - Germline, Ancient DNA, Somatic, and SARS-COV2. Select the steps of analysis to run, the type of compute to use (Parabricks, Sentieon, or open-source), and then upload your data files.


4. Select a reference genome to compare the input data to. You may also optionally upload a BED file detailing genomic regions of note.

5. Tune additional parameters related to your workflow run. These parameters may change depending on your input data.

6. Give your workflow run a unique name, and review the input data and run parameters. When ready to submit, click Run Workflow.

Results Walkthrough

1. To view the results of your Germline Variant Analysis workflow, first find and select your workflow run in the Activity tab.
2. Under the Files tab, you can view the final HTML file, which is nested in the output folder. You may view or download this file. This file can also be found in the File Explorer.