miRNA, ChIP-Seq, SAGE & DGE analysis
NextGENe Software includes unique tools for analyzing small RNA, (microRNA), ChIP-Seq, SAGE as well as DGE analysis of data from Ion Torrent, Illumina GA, Hi-Seq and MiSeq platforms, Applied Biosystems' SOLiD System and Roche GS FLX, FLX Titanium or Junior systems. 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 bio, DNASTAR SeqMan NGEN®, or academic tools like 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 NextGENe's Peak Identification Tool.
NextGENe 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.
NextGENe software takes full advantage of the short sequencing reads and has tools for analyzing the SAGE tags. SAGE Libraries are available that contain lists of sequence tags associated with particular genes. NextGENe can load these libraries as a reference and align the sequence reads to the appropriate sequence tags. The alignment to the tag library is only performed in the forward orientation of the sequences, no reverse complementation is implemented. Digital gene expression reports are created to show the sequence of each tag, the coverage, gene names, and the location in the genome. New gene tags that are not in the library are also reported. These tags can be added to the reference library as novel tags.
For More Information Review
or Download Application notes:
Serial Analysis of Gene Expression (SAGE) Application Note
Digital Gene Expression Application Note
ChIP-Seq_Analysis with NextGENe software
SOLiD System ChIP-Seq Analysis with NextGENe software
Whole Genome Alignment with NextGENe software
Small RNA Application Note
Sequence Analysis Using Barcode/Index Tags of Pooled Samples with NextGENe Software
Using NextGENe software's Pipeline Automation Tool
Plugin for Torrent Browser automation
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