Consulting Services

Bioinformatics Consulting Service at GHTF

Next Generation Sequencing (NGS) technologies are revolutionizing biology. However, analyzing NGS data requires dedicated bioinformaticians who are often not available in many labs. At UCI GHTF, we can help you overcome the challenges of analyzing increasingly large and complex NGS data. We can help you design and analyze a wide variety of high throughput experiments including:

DNA re-sequencing

RNA-Seq

CHIP-Seq

SNP and Indel discovery

Genome and transcriptome assembly

Microarray data analysis

The GHTF provides basic consulting on data analysis approaches and performs defined data analysis routines (recharge basis).

How it works:

  • Upon inquiry and following consultation each user will be provided a Project Agreement along with his/her quotation. The Project Agreement is to be signed by the user. Along with the quotation, this Project Agreement describes our understanding of the work to be carried out by the Facility, methods/software that will be used as well as the expected deliverables and formats. For routine projects it states explicitly that we consider this "fee-for-service" work and not a scientific collaboration.
  • In instances where prior consultation has indicated the need for greater scientific input from the Facility, i.e. collaboration, the Project Agreement will outline the Facility's expectations with respect to publication.

Prioritization

  • Our general policy is first-come, first-served. In any event, the Project Agreement will indicate our estimate of start and completion dates. Users will be notified of any significant deviations from those dates.

Storage

 

  • Due to limited resources, GHTF will store your processed data for two months starting from the date the results are delivered. Clients are responsible for downloading a copy of raw data from IGB where web links will be avaiable for two months.  

For detailed questions please contract:

Dr. Jenny Wu

Director, Bioinformatics

Chao Family Comprehensive Cancer Center

Email: jiew5@uci.edu

Phone: 949-824-6023

 

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DNA re-sequencing (exome sequencing, targeted resequencing,etc.)

  • Quality check of sequencing data, sequence trimming if necessary
  • Reads alignment to reference
  • Statistical summary of reads and alignment
  • Variant Identification and annotation
     

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RNA-Seq

  • Quality check of sequencing data, sequence preprocessing
  • splice aware alignment to reference
  • Statistical summary of reads and alignments
  • Alignment visualization
  • Transcriptome assembly, transcript abundance quantifications and gene fusion identification
  • Identification of differentially expression, differentially spliced isoforms and differentially regulated genes across multiple samples
  • Downstream pathway enrichment analysis, Gene Set Enrichment Analysis

   

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CHIP-Seq

  • Quality check of sequencing data, sequence trimming if necessary
  • Reads alignment
  • Statistical summary of reads and alignments
  • Peak discovery and Peak distribution patterns
  • Peak visualization
  • Motif discovery
  • Data integration with RNA-seq

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SNP and Indel discovery

  • Quality check of sequencing data, sequence trimming if necessary
  • Reads alignment to reference
  • Statistical summary of reads and alignments
  • SNP and Indel discovery vs. reference genome, tumor vs. normal
  • SNP and Indel annotation (exonic, intronic, splicing etc) and filtering (dbSNPs, 1000 Genome etc) and annotation(CADD,SIFT)
  • SNP and Indel summary table and visualization
     

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de novo Whole Genome and transcriptome assembly

  • Quality check of sequencing data, sequence trimming if necessary
  • Reads de novo assembly
  • Statistical summary of assembled contigs
  • Comparison of different assembly
  • Assembled contigs visualization
  • Genome and transcriptome annotation
     

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Microarray data analysis

  • Experimental design
  • Identification of differentially expressed genes
  • Pathway analysis, Gene Set Enrichment Analysis
  • ANOVA and MANOVA