SeqMINER: A genome wide mapping data interpretation platformHere, we present seqMINER, an integrated user friendly platform that allows addressing central questions in the ChIP-seq analysis workflow. The design of seqMINER was made in order to make it as easy as possible for an investigator to reach high level of interpretation on his dataset to answer its biological question at best.
The purpose of seqMINER is to allow qualitative and quantitative comparisons between a reference set of genomic positions and multiple ChIP-seq datasets.
Different analysis modules have been implemented to allow highlighting of general as well as specific patterns in a given dataset. Starting from a set of reference coordinates that can be a list of ChIP-seq enrichment clusters (peaks) for a particular target (i.e. a transcription factor), seqMINER proposes two complementary methods to analyse the signal enrichment status in multiple other tracks:
i) a qualitative method that computes a density array over a defined window around the reference coordinate.
ii) a quantitative method that computes enrichment value over a defined window around the reference coordinate.