.. _`grch38-canonical-transcript-features-gencode-v1`:

grch38-canonical-transcript-features-gencode-v1
===============================================

|downloads|

Protein Coding Canonical Transcript Features for each protein coding gene id from GENCODE's v34 (Ensembl 100) comprehensive set of gene anntotations. Canonical Transcripts are determined using the APPRIS annotation dataset. In short, for all protein coding transcripts, transcripts are filtered based on APPRIS isoform flags. If multiple transcripts of the same gene have equal flags, the isoform with the most exons is chosen. If all transcritps for a gene are not annotated by APPRIS, the transcript with the most exons is chosen as the canonical transcript. APPRIS flag information can be found here: http://appris-tools.org/#/downloads or here: https://uswest.ensembl.org/info/genome/genebuild/transcript_quality_tags.html. Features include: gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine.

================================== ====================================
GGD Package                        grch38-canonical-transcript-features-gencode-v1 
Species                            Homo_sapiens
Genome Build                       GRCh38
GGD Channel                        ggd-genomics
Package Version                    1
Recipe Author                      mjc 
Data Provider                      GENCODE
Data Version                       release-34_03-24-2020
Genomic File Type                  gtf
Data file coordinate basing        1-based-inclusive
Package's Data Files               grch38-canonical-transcript-features-gencode-v1.gtf.gz, grch38-canonical-transcript-features-gencode-v1.gtf.gz.tbi
Approximate Size of Each Data File grch38-canonical-transcript-features-gencode-v1.gtf.gz: **10.74M**, grch38-canonical-transcript-features-gencode-v1.gtf.gz.tbi: **262.63K**
Package Keywords                   Canonical, Canonical-Transcripts, Canonical-Isoforms, Gene-Features, GTF, Gene-Features, Gene-Annotations, GTF, GENOCDOE-GTF, GENCODE-Gene-Sets, Annotated-Transcripts
Package Dependencies:              gsort, htslib, zlib
Recipe                             https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Homo_sapiens/GRCh38/grch38-canonical-transcript-features-gencode-v1
================================== ====================================

Install with ``--prefix``
-------------------------
**Prefix install enabled:** *True*

Installation
------------

.. highlight: bash

With ggd installed and an activated ggd channel (see :ref:`using-ggd`), install with::

   ggd install -c genomics grch38-canonical-transcript-features-gencode-v1 

.. |downloads| image:: https://anaconda.org/ggd-genomics/grch38-canonical-transcript-features-gencode-v1/badges/downloads.svg
               :target: https://anaconda.org/ggd-genomics/grch38-canonical-transcript-features-gencode-v1

Activating Environment Variables
--------------------------------

Run :code:`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 :code:`ggd get-files` to access this package's
    data files.