The pipeline takes alignment bam files (processed from ChIP-seq Mapping Pipeline) from replicates and its control experiment to produce several outputs: Signal tracks’ depicting control-normalized tag …

genome@soe.ucsc.edu Outline • Browser Basics • Tools for finding ENCODE data • Annotating a BED file: RNAseq example • Annotating a VCF file • Track Hubs: What are they? How do I make one? • …

ENCODE has worked up a common pipeline that can be used for ENCODE RNA-Seq assays, using the STAR mapper. It is deployed on the DNANexus Environment and also available in a GitHub …

Usage: Below is a description of all fields required to be filled out in the manifest file. See https://github.com/YeoLab/merge_peaks/blob/master/example/204_RBFOX2.yaml for a full example …

The ENCODE Registry of ccREs and SCREEN Jill Moore, PhD Henry Pratt, MD/PhD student

The NIH Roadmap Epigenomics Program Kim McAllister mcallis2@niehs.nih.gov Program Administrator Genes and Environment Health Branch National Institute of Environmental Health Sciences

RSEM Documentation Includes Name, Synopsis, Arguments, Basic Options, Advanced Options, Description of RSEM, Outputs, and Examples.

in situ Hi-C Experimental Standards of the ENCODE Consortium Crosslinking Grow two to five million mammalian cells under recommended culture conditions to about 80% confluence. Pellet suspension …

To run ChromHMM starting from aligned .bam files, for different histone modifications, (for example downloaded from the ENCODE portal) some additional steps are required before running the …

Single-End ATAC-seq parameters with CSEM : function _bowtie2_csem()