21646344
This reference describes BEADS.
| PMID | PMID 21646344 |
|---|---|
| Title | Systematic bias in high-throughput sequencing data and its correction by BEADS. |
| Year | 2011 |
| Journal | Nucleic Acids Research |
| Author | Cheung MS, Down TA, Latorre I, Ahringer J. |
| Volume | |
| Start page |
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Full text description
Genomic sequences obtained through high-throughput sequencing are not uniformly distributed across the genome. For example, sequencing data of total genomic DNA show significant, yet unexpected enrichments on promoters and exons. This systematic bias is a particular problem for techniques such as chromatin immunoprecipitation, where the signal for a target factor is plotted across genomic features. We have focused on data obtained from Illumina's Genome Analyser platform, where at least three factors contribute to sequence bias: GC content, mappability of sequencing reads, and regional biases that might be generated by local structure. We show that relying on input control as a normalizer is not generally appropriate due to sample to sample variation in bias. To correct sequence bias, we present BEADS (bias elimination algorithm for deep sequencing), a simple three-step normalization scheme that successfully unmasks real binding patterns in ChIP-seq data. We suggest that this procedure be done routinely prior to data interpretation and downstream analyses.
