ABSTRACT
Visualisation of the data generated throughout the analysis is essential to get an impression of data quality, understand the results and integrate the data with other information. Instead of visualising each single read, a genomic coverage file can be generated to summarise the number of reads overlapping each position in the genome. Visualisation of the reads can already be carried out after genomic alignment. BAM files containing the aligned reads can be loaded directly into genome browsers. In regions with high read density such as peaks, where hundreds of reads align, such a visualisation does not scale well. The University of California Santa Cruz genome browser is available online or can be installed locally. The Integrative Genomic Viewer developed at the Broad Institute is a popular alternative that can be run locally.
