Reviews on different NGS data analysis methods. LaTeX Beamer format.

• atacseq - summary on ATAC-Seq processing methods
• chipseq - summary on ChIP-Seq processing from qc to replicated peak calling
• differential_chipseq - how to compare replicated data
• peaks - notes on peaks classification by length based on small subset of Roadmap Epigenomics data

ENCODE standards https://www.encodeproject.org/data-standards
ENCODE Rest API https://www.encodeproject.org/help/rest-api
ENCODE DNANexus pipelines source https://github.com/ENCODE-DCC

ChIP-seq analysis notes from Tommy Tang https://github.com/crazyhottommy/ChIP-seq-analysis