LinDA is a high-fidelity, single-tube Linear DNA amplification method for ChIP-seq and other genome-wide studies based on massive parallel sequencing.

Shankaranarayanan P, Mendoza-Parra MA, Walia M, Van Gool W, Wang L, Li N, Trindade LM and Gronemeyer H.

Single-tube linear DNA amplification (LinDA) for robust ChIP-seq. Nature Methods. 2011 Jun 5;8(7):565-7

Single-tube linear DNA amplification (LinDA) for genome-wide studies using a few thousand cells. Nature Protocols (manuscript in revision)

Sequential chromatin
immunoprecipitation protocol for global analysis through massive parallel sequencing (reChIP-seq)) Protocol exchange, DOI 10.1038/protex.2011.256

MeDiChI-seq is a regression-based method for peak detection in the context of profiling of protein-chromatin interaction patterns. As the first step MeDiChI computes a model of multiple binding events present in a particular ChIP-seq profile. Likely binding events are then identified by comparison of particular peak with the model. Predicted binding events are further characterized in the context of their significance by the non-parametric bootstrapping statistical approach.

ChIP-seq
-massive para-llel sequencing
-Peak caller

Manuscript in prepara-
tion.

Comparative analysis between ChIP-seq and other NGS datasets requires prior characterization of their degree of technical similarity. NGS Q/C Generator infer Quality indicators from the distribution of sequenced reads associated to a particular NGS profile. Such information is then used for comparative purposes and for defining strategies aiming to improve the quality of the sample-derived datasets.

Manuscript in prepara-
tion.