grch38-segmental-dups-ucsc-v1

Segmental duplications (SuperDups) File from UCSC. That is, duplications of at least 1kb total sequence of non-repeatmasker sequence in bed format. Remapped from UCSC hg38 to Ensembl GRCh38.

GGD Package	grch38-segmental-dups-ucsc-v1
Species	Homo_sapiens
Genome Build	GRCh38
GGD Channel	ggd-genomics
Package Version	1
Recipe Author	mjc
Data Provider	UCSC
Data Version	19-Oct-2014
Genomic File Type	bed
Data file coordinate basing	0-based-inclusive
Package’s Data Files	grch38-segmental-dups-ucsc-v1.bed.gz, grch38-segmental-dups-ucsc-v1.bed.gz.tbi
Approximate Size of Each Data File	grch38-segmental-dups-ucsc-v1.bed.gz: 4.14M, grch38-segmental-dups-ucsc-v1.bed.gz.tbi: 79.50K
Package Keywords	superdups, segdups, seg, dups, duplications, UCSC, Segmental-Duplication
Package Dependencies:	grch38-chrom-mapping-ucsc2ensembl-ncbi-v1, gsort, htslib, zlib
Recipe	https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh38/grch38-segmental-dups-ucsc-v1

Install with --prefix

Prefix install enabled: True

Installation

With ggd installed and an activated ggd channel (see Using GGD), install with:

ggd install -c genomics grch38-segmental-dups-ucsc-v1

Activating Environment Variables

Run source activate base after installing the data package to activate the environment variables associated with this data package.

Note

You must be in the conda environment where the data package was installed in order to use the associated environment variables. Otherwise, use ggd get-files to access this package’s data files.