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Peak calling with MACS2 | Introduction to ChIP-Seq using high-performance computing

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Peak calling, the next step in our workflow, is a computational method used to identify areas in the genome that have been enriched with aligned reads as a consequence of performing a ChIP-sequencing experiment. For ChIP-seq experiments, what we observe from the alignment files is a strand asymmetry with read densities on the +/- strand, centered around the binding site. The 5’ ends of the selected fragments will form groups on the positive- and negative-strand. The distributions of these groups are then assessed using statistical measures and compared against background (input or mock IP samples) to determine if the site of enrichment is likely to be a real binding site. </div> Image source: Wilbanks and Faccioti, PLoS One 2010 There are various tools that are available for peak calling. One of the more commonly used peak callers is MACS2, and we will demonstrate it in this session. Note that in this Session the term ‘tag’ and sequence ‘read’ are used interchangeably. NOTE: Our datase

Peak calling with MACS2 | Introduction to ChIP-Seq using high-performance computing Skip to the content. Contributors: Meeta Mistry, Radhika Khetani Approximate time: 80 minutes Learning Objectives Describe the different components of the MACS2 peak calling algorithm Describe the parameters involved in running MACS2 List and describe the output files from MACS2 Peak Calling Peak calling, the next step in our workflow, is a computational method used to identify areas in the genome that have been enriched with aligned reads as a consequence of performing a ChIP-sequencing experiment. For ChIP-se

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