Next Generation Sequence Analysis flow chart:

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Standard Bioinformatic Analysis

Gene Arrays standard bioinformatics analysis is currently included in the price of all the sequencing projects using proprietary Illumina pipeline software, this includes:

  • Image analysis to identify individual clusters of reads
  • At each cycle of the sequencing run, using the relative intensity levels at each cluster to perform Base-Calling
  • Generation of sequence reads with associated quality scores for each base
  • Generation of filtered read data, based on the per-base quality scores
  • Generation of a customised Pipeline report, summarising run statistics and quality control analysis

Advanced Bioinformatic Analysis

Alignment to Reference Sequence

  • Mapping of all reads to a specified reference genome
  • Statistic report detailing coverage, orientation of mapped reads, and numbers of unmapped reads
  • Summary of coverage available in both graphical and tabular format

Visualizing sequence data within a genome browser

Re-sequencing and polymorphism detection

  • Mutation detection in samples
  • Novel mutation discoveries
  • Annotation of sequence polymorphisms
  • Functional analysis of target genes

ChIP Sequencing

  • ChIP-seq analysis to determine genomic regions and peaks
  • Annotation of ChIP-seq regions and Peaks
  • Sequence motif analysis
  • Functional analyses of ChIP-seq target genes

RNA Sequencing

  • Identification of exon splice crossing sequencing reads
  • Identification of the differences in gene expression between the control and treated samples
  • Identification of the differences in alternative splicing between the control and treated samples
  • Full gene annotation

Small RNA Sequencing

  • Discovering microRNAs and analysis
  • Discovering novel microRNAs from deep sequencing data using RNA secondary structure information

Have any questions? Call us or Request a Quote

If you have any questions? Help with Experimental Design? Price Quote? Have any questions related to Genome sequencing, Microarrays and Bioinformatic Support, contact us.


  • Gene Arrays, provides microarray & sequencing services and their technical team is very good and co-operative. Asked them for advanced analysis of microarray data from human and cell lines, they did very good job and very fast turnover time. Thank you "Gene Arrays", I recommend to go with them.
    Amit Tiwari, PhD
  • I spoke with technical team for experimental design for microarrays (GEP) and ChIP-seq. Tech team help me for advanced microarray data analysis and ChIP-seq data so quickly. Thank you and I recommend to take services from Gene Arrays.
    Dr. Roger Farewell, MD


Company Info:

Gene Arrays
Vedic Research Inc.


1975 Washington Ave,
Seaford, NY 11783

Phone number:

+1 (917) 719-0012


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