Ben_Fairfax_Circos

ChIP-Seq Analysis

mm9_plxnd1_UCSC_image_ChIPFigure shows transcription factor binding at the mouse mm9 PLXND1 gene.

ChIP-seq combines chromatin immunoprecipitation (ChIP) with deep sequencing to identify the binding sites of DNA-associated proteins and modifications in an organism.

The Oxford Genomics Centre's  bioinformatics unit use established analysis pipelines to assist the customer in the interpretation of ChIP-seq data. All sequencing data are first aligned using the the alignment tool STAMPY  and then analysed using MACS to identify significant peak locations within the genome. The following files will be provided with ChIP-seq data:

 

  • Primary QC report  - A file of general QC metrics for each sample sequenced.
  • Secondary QC report  - A file of QC metrics to assess the enrichment of the IP and specificity of mapping to the genome in each sample.
  • FASTQ file - A file of unmapped sequenced reads for each sample.
  • A BAM file - An alignment report of sequenced read mapping results.
  • Peaks.xls file: A file containing information about called peaks.
  • Peaks.bed:  A file of peak locations to enable the customer to view peak locations in a a browser such as UCSC. 
  • Annotated.bed: A file containing information about the peaks and closest downstream genes for each genomic locus.

 

Optional analyses available:

  •    Differential Peak calling
  •    Motif finding
  •    Custom Analyses

 

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