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Assessing peaks is a central step of the analysis to determine specific signal over the noise background for the identification of real binding sites. The number of identified peaks increases with the sequencing depth because weaker sites become statistically significant with a greater number of reads (Sims et al., 2014). However, the optimal sequencing depth can only be experimentally evaluated, as it depends on the noise background of the antibody (Nakato and Shirahige, 2017).
(Sims et al., 2014) Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet.
(Nakato and Shirahige, 2017) Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation. Brief Bioinform.
(Bottini et al., 2017) Recent computational developments on CLIP-seq data analysis and microRNA targeting implications. Brief Bioinform.