ChIP-Seq

A ChIp-Seq workflow starts with getting some basic information on the data (read length, number of reads, global quality of dataset). Then, we map each read to the reference genome to obtain the coordinates. Next we define the peaks i.e. the region with a high density of reads, where the studied factor was bound and we visualize the results to facilitate the biological interpretation. Motif discovery algorithms can be applied to extract significant motifs from the sequences. Discovered motifs can be used to screen databases to identify potentially bound transcription factors and/or target genes.