miRNA, ChIP-Seq, & DGE analysis
NextGENe software includes unique tools for analyzing small RNA, (microRNA), ChIP-Seq as well as DGE analysis of data from Illumina® iSeq, Miniseq, MiSeq, NextSeq, HiSeq, and NovaSeq systems, Ion Torrent Ion GeneStudio S5, PGM, and Proton systems as well as other platforms. The NextGENe Viewer provides biologists with the ability to review results in detail. This high level of visualization is not available in programs such as CLC Genomics Workbench, Lasergene's SeqMan Pro, as well as academic software such as MAQ & SOAP, Top Hat, BWA & Bowtie. Peak detection settings can also be manually adjusted by the user using the Peak Identification Tool in the viewer.
MicroRNA sequencing data can be aligned to the miRBase reference to detect the presence of known miRNAs, with expression levels for each miRNA sequence reported. Alternatively any small RNA sample dataset can be mapped against a genomic reference to detect novel small RNAs using the NextGENe Peak Identification Tool.
NextGENe software also includes software tools specially designed to handle chromatin immunoprecipitation DNA sequencing data (ChIP-Seq). These tools work by aligning sample data to the reference sequence, utilizing coverage for peak detection and providing a specialized peak report which includes detailed information about each peak.
When alignment and initial peak detection is completed, the results are shown in the NextGENe Viewer with peaks highlighted. The NextGENe Viewer provides biologists with the ability to review results in detail.
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