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 specifi c 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.
CITATION STYLE
Ye, T., Ravens, S., Krebs, A. R., & Tora, L. (2014). Interpreting and visualizing ChIP-seq data with the seqMINER software. Methods in Molecular Biology, 1150, 141–152. https://doi.org/10.1007/978-1-4939-0512-6_8
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