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 …

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 …

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 …

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 …

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 …

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. …

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 …

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