Interpreting and visualizing ChIP-seq data with the seqMINER software

Methods Mol Biol. 2014;1150:141-52. doi: 10.1007/978-1-4939-0512-6_8.

Abstract

Chromatin immunoprecipitation coupled high-throughput sequencing (ChIP-seq) is a common method to study in vivo protein-DNA interactions at the genome-wide level. The processing, analysis, and biological interpretation of gigabyte datasets, generated by several ChIP-seq runs, is a challenging task for biologists. The seqMINER platform has been designed to handle, compare, and visualize different sequencing datasets in a user-friendly way. Different analysis methods are applied to understand common and specific binding patterns of single or multiple datasets to answer complex biological questions. Here, we give a detailed protocol about the different analysis modules implemented in the recent version of seqMINER.

MeSH terms

  • Biostatistics / methods*
  • Chromatin Immunoprecipitation / methods*
  • Cluster Analysis
  • Computer Graphics*
  • High-Throughput Nucleotide Sequencing / methods*
  • Software*