Next Generation Sequencing

Easily Analyze Your Next Generation Sequencing Data with Partek Genomics Suite

Next generation sequencing enables accurate quantification of molecules, taking trancriptomics analysis in Partek Genomics Suite (Partek GS) beyond gene expression, into quantification at the transcript level, novel transcript discovery, alternative splicing and quantification at the exon level. Also non coding RNA, like miRNA are analyzed. Through sequencing, genotype information at the SNP level is obtained, extending the analysis further to allele specific expression and SNP discovery.

Partek GS empowers biologists to analyze RNA-Seq, ChIP-Seq, Methyl-Seq and DNA-Seq easily by following dedicated workflows within one software, with one familiar interface, across: Data import > Quality Control > Statistical Analysis > Clustering > Gene Ontology and Pathway analysis - with highly interactive and intuitive visualizations, dedicated genome browser and data analysis reporting features.

This is just the beginning, as functional genomics pushes for larger understanding of the cell and underlying regulatory mechanisms. Combining epigenome, genome and transcriptome data offers the biologist an instrumental tool in confirming hypothesis, across the various compartments of the cell. Partek GS provides Integrated Genomics workflows, that empower systems biology, across technologies like NGS and microarray as well as across assays with focus on DNA, RNA or DNA-protein interactions, such as detecting peaks, performing novo motif discovery, comparing with downstream gene or transcript expression and much more.

At the core of Partek GS, annotations are processed efficiently to enable the correlation of the various data formats and save you time. Try Partek Genomics Suite for your next generation sequencing data.

Specific Applications for Next Generation Sequencing in Partek Genomics Suite

ChIP-Seq Analysis

Partek GS will identify regions of the genome where short reads pile up to create a peak representing a binding site of the protein of interest from aligned reads. Once the peak regions are defined, these sequences can be searched for motifs. De novo motifs can be discovered and visualized. Alternatively, a collection of known motifs can be screened to see what is common across the peaks based on sequence content. Also, find overlapping gene tools within Partek GS will help you overlap your enriched regions to gene annotation for functional group enrichment studies.

RNA-Seq Analysis

Using a whole-transcriptome sequencing approach, sequence data are analyzed for differential expression and alternative splicing based on known mRNA annotation. Sequencing reads that are not mapped to any known mRNA annotation are used to uncover the novel transcriptional regions. Partek GS will identify and quantify sequence variants (coding SNPs) within RNA-seq samples. With a collection of SNPs identified, Partek GS will then find allele specific expression that drive phenotypic change within the transcriptome. Both paired end and junction reads are supported.

microRNA-Seq Analysis

Partek GS enables the differential expression of known microRNAs (miRNA) between different samples. Map your reads to known miRNA databases to indentify novel miRNAs. You can also integrate your miRNA data with gene expression data to identify a potential correlation of your miRNAs of interest and their target mRNAs.

DNA-Seq Analysis

From your targeted re-sequencing data, SNPs can be identified and visualized. Partek GS will map your SNP result to gene annotation for novel discoveries.