BEADS

BEADS is a software tool that aims to correct the systematic bias in the distribution of genomic sequences across the genome, a significant issue for techniques such as chromatin immunoprecipitation. This is essential since genomic sequences obtained through high-throughput sequencing are not uniformly distributed across the genome. For instance, total genomic DNA sequencing data show significant enrichments in promoters and exons. The systematic bias can be attributed to factors such as GC content, mappability of sequencing reads, and regional biases generated by the local structure.

In particular, this bias is a problem for techniques such as chromatin immunoprecipitation, where the signal for a target factor is plotted across genomic features. Relying on input control as a normalizer is not generally appropriate due to sample-to-sample variation in bias. BEADS provides a simple three-step normalization scheme to address this issue that unmasks real binding patterns in ChIP-seq data. This normalization scheme is designed to correct sequence bias, and it is suggested that this procedure be done routinely before data interpretation and downstream analyses.

BEADS focuses on data from Illumina's Genome Analyzer platform, where at least three factors contribute to sequence bias. These factors include GC content, the mappability of sequencing reads, and regional biases generated by the local structure. The software tool presents a straightforward and effective method to address this issue, which is essential for accurate data interpretation.