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NGS: RNA-Seq, De-novo and Reference assembly, Metagenomics, SNP analysis, Exome-Seq, ChIP-Seq

Our experience with original in-house research has enabled us not only to perform comprehensive analysis of various types of NGS data, but also to present it in such a way that can be easily understood by other biologists, and the scientific objectives are addressed correctly. This aspect, in fact, makes us unique as service providers in the area of data analysis. Although we primarily take up data analysis services, we also undertake end-to-end services for designing experiments, NGS work, and primary, secondary, and tertiary data analysis. In fact, such projects have been more satisfying in instances when scientists had to approach us after disappointment from other service providers who neither guided them correctly for designing experiments nor concluded the data analysis. We have successfully completed multiple NGS projects.

RNA Sequencing
Illustrative list of tasks
  • Quality analysis
  • Adapter and Quality trimming
  • Abundance estimation
  • Novel miRNA identification
  • Differential expression
  • Other small RNA identification
  • Statistical analysis
  • miRNA target prediction
  • Functional annotation of miRNA targets: Gene Ontology, Pathways
  • Report with publication quality tables and figures
Example(s) of completed projects
  • miRNA data analysis and target prediction of a rodent species for a research group at CCMB, Hyderabad, India.
  • miRNA data analysis and target prediction of drug treated lung cancer cells for a research group at CHG, Bengaluru, India.
In house research
  • Comparison of known and predicted miRNA resources
  • Compilation of resources with their features for miRNA analysis (www.startbioinfo.com)

Non-coding RNA sequencing (e.g., miRNA, lncRNA)
Illustrative list of tasks
  • Quality analysis
  • Data trimming/filtering
  • Data normalization
  • Abundance estimation: Gene and Transcript quantification
  • Novel transcripts and splice forms identification
  • Differential expression
  • Statistical analysis
  • Identification of fusion genes and trans-splicing
  • Functional annotation: Gene Ontology, Pathways, Domains
  • Report with publication quality tables and figures
Example(s) of completed projects
  • Transcriptome analysis of Arabidopsis for a research group at KISR, Kuwait.
  • RNA-Seq data analysis and functional analysis of a rodent species for a research group at CCMB, Hyderabad, India.
  • Transcriptome analysis of CHO derived cell lines for a private company, Bengaluru, India.
  • Identification of chromosome specific transcripts in human, mouse, and Drososphila, for a research group at CCMB, Hyderabad, India.
In house research

De-novo transcriptome assembly and annotation
Illustrative list of tasks
  • Quality analysis
  • Data trimming/filtering
  • Transcriptome assembly
  • Annotation: Coding regions, ORFs, Peptide sequences, Homolog
  • Abundance estimation: Gene and Transcript quantification
  • Differential expression
  • Statistical analysis
  • Functional annotation: Gene Ontology, Pathways, Domains
  • Report with publication quality tables and figures
Example(s) of completed projects
  • De-novo transcriptome analysis of CHO derived cell lines for a private company, Bengaluru, India.
  • De-novo transcriptome assembly and annotation of a plant species for a company in India.
  • De-novo transcriptome assembly and identification of trans-splicing events in human, mouse and Drosophila, for a research group at CCMB, India.
In house research

Reference assembly
Illustrative list of tasks
  • Quality analysis
  • Data trimming/filtering
  • Genome/Transcriptome alignment
  • Report with publication quality tables and figures
Example(s) of completed projects
  • Reference sequence assembly and analysis [multiple projects]
In house research

De-novo genome assembly and annotation
Illustrative list of tasks
  • Quality analysis
  • Data trimming/filtering
  • De-novo genome assembly
  • Repeat annotation
  • Gene structure prediction
  • Non-protein coding gene prediction
  • Synteny analysis
  • SNP analysis
  • Functional annotation
  • Orthologous gene analysis
  • Phylogenetic analysis
  • Report with publication quality tables and figures
Example(s) of completed projects
  • De-novo genome assembly, annotation, and data submission of a commercial fish species for a research group abroad.
In house research

SNP analysis
Illustrative list of tasks
  • Quality analysis
  • Data trimming/filtering
  • Genome/Transcriptome alignment
  • SNP and Indel identification
  • Report with publication quality tables and figures
Example(s) of completed projects
  • De-novo genome assembly and SNP analysis of a commercial fish species for a research group abroad.
In house research

Metagenomics
Illustrative list of tasks
  • Quality analysis
  • Data trimming/filtering
  • Taxonomic classification
  • Operational Taxonomic Units (OTUs) generation
  • Statistical analysis: Diversity indexes
  • Visualizations
  • Functional annotation: Gene Ontology, Pathways
  • Report with publication quality tables and figures
Example(s) of completed projects
  • Metagenomics analysis of sequencing data from treated plant samples, for a research group at KISR, Kuwait.
  • Metagenomics analysis of time-series sequencing data from plant samples, for a research group at KISR, Kuwait.
  • etagenomics analysis of sequencing data from NGS & Sanger's method in the context of human gut microbiome for a medical research group in India.
In house research

ChIP Sequencing
Illustrative list of tasks
  • Quality analysis
  • Data trimming/filtering
  • Genome alignment
  • Statistical analysis to explore ChIP enrichment and sample correlation
  • Peak calling/Enriched binding regions and Visualization
  • Identification of differential peaks/binding regions
  • Annotation of nearest Transcriptional start site (TSS)
  • Functional analysis of differentially enriched genes
  • Report with publication quality tables and figures
Example(s) of completed projects
  • ChIP-Seq data analysis of mouse brain samples, for a research group at CCMB, Hyderabad, India.
  • ChIP-Seq data analysis for a research group at KMIO, Bengaluru, India.
In house research

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