grch38-self-chain-ucsc-v1

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Self chain alignemnts of the human genome with an improved gap scoring system. Alignemtns point out areas of duplication wihtin the human genome, with the exception of the pseudoautosomal regions on X and Y. From the Human Chained Self Alignemnts track on UCSC. Remapped from UCSC hg38 to Ensembl GRCh37

GGD Package

grch38-self-chain-ucsc-v1

Species

Homo_sapiens

Genome Build

GRCh38

GGD Channel

ggd-genomics

Package Version

1

Recipe Author

mjc

Data Provider

UCSC

Data Version

06-Mar-2014

Genomic File Type

bed

Data file coordinate basing

0-based-inclusive

Package’s Data Files

grch38-self-chain-ucsc-v1.bed.gz, grch38-self-chain-ucsc-v1.bed.gz.tbi

Approximate Size of Each Data File

grch38-self-chain-ucsc-v1.bed.gz: 790.34M, grch38-self-chain-ucsc-v1.bed.gz.tbi: 700.77K

Package Keywords

Self-Chain, Self-Alignment, Repeats, low-copy-repeats

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-self-chain-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-self-chain-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.