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Informative sequence based models for fragment distributions in ChIP seq, RNA seq and ChIP chip data

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Figure

Figure 1-3Processing and amplification of DNA fragments for use in the Illumina sequencer.a) Double stranded DNA fragments are repaired by extending 3’ excessive ends and digesting 3’protruding ends
Figure 1-4Amplification and sequencing of fragments on the flow cell.the DNA is denatured and run over the flow cell which is covered with a lawn of primers (red and blue)corresponding to the sequence of one the two adaptors and the complement of the other
Figure 1-7RNA fragment is converted to a slightly shorter double stranded DNA fragment
Figure 2-5Representation of core Nelder-Mead optimisation stepa) Set of vectors each
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Outline

An introduction to the RNA-seq protocol Summary of data sources †‡ There is a significant sequence-dependent bias in fragment start locations Adjustment of fragment distribution for sequence bias Selecting only a subset of the sequences reduces ‘noise’ from low sequence Discussion Cooperative effects between adjacent binding sites at specific site spacings Obtaining information about protein binding from ChIP-seq data

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