Standard Analysis Services at McDermott Bioinformatics Lab
At the McDermott Bioinformatics Lab, we offer comprehensive standard analysis services for various types of sequencing data. Our goal is to provide high-quality, reproducible results, with a focus on both data integrity and insightful interpretation.
RNA Sequencing Analysis
We process the following data for RNA sequencing:
- Raw Data: gzipped FASTQ files (unprocessed)
- Quality Control: FASTQC report with basic sequencing quality metrics
- Mapping & Alignment: Mapped BAM files (standard format) & alignment report
- Data Normalization: Bigwig files for coverage visualization
- Statistical Analysis:
- Clustering and dendrogram visualization
- MDS plot, MA plot, and Volcano plot
- EdgeR output for differential expression analysis
ChIP Sequencing Analysis
For ChIP-Seq data, we provide:
- Raw Data: gzipped FASTQ files (unprocessed)
- Quality Control: FASTQC report with basic sequencing quality metrics
- Mapping & Alignment: Mapped BAM files
- Data Normalization: Normalized wiggle and bigwig files
- Quality Measures: PhantomPeakQualTools for ChIP-Seq quality assessment
- Analysis Outputs:
- HOMER-generated analysis output
- MACS2 peak calling files
- Peak annotation files
Exome Sequencing Analysis
Our Exome sequencing services include:
- Raw Data: gzipped FASTQ files (unprocessed)
- Quality Control: FASTQC report with basic sequencing quality metrics
- Mapping & Alignment: Mapped BAM files
- Mapping Statistics: Detailed mapping statistics
- Metrics: PICARD metrics, coverage statistics (including plots, target region coverage, and mean coverage)
- Variant Calling: Annotated VCF and tab-delimited files for variant calls
CRISPR Analysis
We provide CRISPR screen analysis, including:
- Raw Data: gzipped FASTQ files
- Quality Control: FASTQC report
- Normalized Counts: sgRNA representation quantification
- Gene & sgRNA Summary: Results for comparisons
- Customized Analysis: Using tools like MAGeCK
Single Cell Analysis
We provide analysis for single-cell sequencing data, including:
- Count Results: Available in the output folder
- Summary Reports: Sequencing, mapping, and sample information
- BAM Files: Sample-wise alignment data
- Cloupe Files: Visualization with Cloupe browser
- Multiomic Analysis: Secondary analysis results from Cell Ranger ARC
Custom Analysis Services
In addition to our standard analysis offerings, we can tailor bioinformatics pipelines to meet the unique needs of your project. Custom analyses are designed for cases that fall outside the scope of our standard pipeline and may include:
- Custom Genome Mapping: Mapping to a non-standard genome reference
- Non-standard Software: Using software tools outside of our pipeline
- External Data: Data not generated by the McDermott Sequencing Core
- Re-analysis: Tweaking software parameters or incorporating additional data into the analysis
- Specialized Analyses: Any analysis not covered by general bioinformatics categories, such as RNA-Seq, ChIP-Seq, Exome sequencing, Amplicon sequencing, Gro-Seq, SmallRNA, or cancer-related sequencing
- Publication-ready Results: Generating high-quality charts, including heatmaps, volcano plots, and hierarchical clustering, tailored to your project’s needs
Advanced Analysis Options
We also provide in-depth analysis for specific scenarios, offering more detailed, manual interventions where automation may not be sufficient. For example:
- Exon Capture/Whole Genome: Custom analysis for specific gene sets or sequencing designs
- Pedigree-based Analysis: Analysis of familial relationships in sequencing data
- ChIP-Seq:
- Filtering enriched gene sets based on project-specific criteria
- Intersection/Union of peaks between conditions
- IP analysis and pathway analysis (e.g., IPA)
- RNA-Seq:
- Alternate sample combinations for differential expression analysis
- Intersection/Union of gene sets between samples/groups
- Further filtering of enriched gene sets based on project-specific criteria
- Pathway analysis (e.g., IPA)
- Xenograft Studies: Specialized analysis for xenograft experiments
If you have specific requirements that are not listed here, please get in touch with us to discuss how we can tailor our analysis to fit your project needs.