ChIP-Seq | Strand NGS


Strand NGS supports a workflow for the analysis and visualization of ChIP-Seq data. The workflow provides the ability to identify transcription factor binding sites and histone modification sites using the PICS and MACS peak detection algorithms. It supports the ability to detect motifs in the peak regions using GADEM, and scan for known motifs in the genome or region of interest. Further downstream analysis such as GO, pathway analysis, etc can be performed on the set of affected genes.

Download the ChIP-Seq Highlights Guide
White paper Calling narrow and broad peaks from ChIP-Seq data in StrandNGS
Watch the ChIP-Seq Webinar Recording

Peak Detection

Identify protein binding sites using two peak finding algorithms, PICS and MACS. View the results in the Genome Browser in the context of known genes.

Discover Significant Motifs

Discover the most significant motifs present in the vicinity of the binding regions using an efficient implementation of the GADEM algorithm. Motifs in JASPAR format can be imported and occurrences of the motifs can be detected by scanning the whole genome.

Affected Genes

Identify genes affected by transcription factor regulation.

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Pipeline Manager

Configurable pipelines for compute-intensive tasks using the Pipeline Manager. Allows interaction with the user interface even as pipeline executes in the background.

GO Analysis

Perform GO analysis to identify significant GO terms for affected genes.

Pathway Analysis

Use the packaged database of 2 million interactions (with supporting PubMed references) to find relationships between genes. Learn more

Compare gene lists

Compare different gene lists from multiple experiments and across organisms.