Bioinformatics

VANTAGE Bioinformatics service provides QC reports for the sequencing quality and per sample yield. The file deliverable is a demultiplexed FASTQ containing the PF reads. Further bioinformatics services are available upon request.

  • Coverage and variant analysis, including annotation of variants is performed on all samples by use of Illumina’s Dragen tool.  Available outputs include VCF/gVCF files, coverage files, aligned BAM, and statistics. 

  • Human whole exome analysis is performed using Illumina’s Dragen pipeline.  Outputs are similar to whole genome analysis, and also include statistics to describe the effectiveness of exome enrichment.  Available outpus include VCF/gVCF files, coverage files, aligned BAM, and statistics. 

    • For 2 condition experimental designs, all alignment and analysis is performed by Illumina’s Dragen RNA pipeline.  The pipeline calculates gene counts per sample and is able to perform pairwise differential gene expression for all annotated genomes.  Outputs include BAM, counts files, and tables of differentially expressed genes.
    • (Additional fees for analysis): For multi-condition experimental designs, additional analysis can be performed for each comparison desired.  Data from Dragen RNA pipeline is used to analyze data in edgeR to generate additional tables and reports.

  • VANTAGE is available to analyze RNAseq projects from non-model organisms, including bacterial genomes, or other genomes not included in Dragen’s databases.  Outputs are similar to outputs for custom analysis above

    • Gene Expression analysis (5’ or 3’ counting):

    All samples are run though the 10X cellranger count pipeline for gene counting.  If multiple samples are submitted, counts are aggregated into a single output for manual inspection using the 10X CLoupe Browser.  Outputs are standard 10X outputs and .loupe file for use in CLoupe.

    • ATAC seq

    ATAC seq samples are analyzed using 10X Cellranger software.  Outputs are cloupe and standard outputs (NEED HELP FROM OTHERS ON THIS)

    • VDJ (+Gene Expression)

    VDJ data are calculated using 10X cellranger vdj software, and can be combined with Gene Expression data.  If multiple samples are submitted, samples will be aggregated for joint analysis.  Outputs are standard cellranger outputs, including cloupe compatible file per project.

    • Sample Barcoding

  • Cell barcoding using any of the following technologies are possible:

      • Cell/sample Hashing
      • Antibody tagging
      • CRISPR

    Each barcoding type will be included in analysis pipelines and combined with other sample analysis.  These data are included in the cloupe outputs, for further analysis.

  • If additional analysis is required, Vantage has tools to reanalyze data.  This includes:

      • Filtering cells to remove low quality data
      • Reclustering cells
      • Custom cell annotations
      • Multi-sample demultiplexing

  • Long ranger is applied to any phased sequencing using the 10X chromium.  (What data are generated?)

    Microbiome Analysis:

                    Microbiome community profiling is available using either 16S or whole shotgun metagenomics.  Analysis is done using either Mothur or Qiime (by investigator’s choice) for 16S data, or using Kraken for shotgun metagenomic data.  Additional options available on request.

    Genome Imputation:

                    Vantage can impute genomic variants from low pass whole genome sequencing (LP-WGS), LP-WGS + Exome, or from genotyping data.  Outputs are vcf files, and logs of imputation steps.  Additional assistance is available.

    Genotyping:

    Vantage performs Quality Assurance and quality control on all genotyping projects, including gender-matching tests, and …. (LANA?)

    Additional Analysis pipelines:

    Vantage also has pipelines to analyze data for

                    ATACseq

                    CutAndRun