KnownGene: Difference between revisions

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== Create work directory ==
== Initialize work directory ==


Create and cd into work directory of the form /hive/data/genomes/$db/bed/gencode$GENCODE_VERSION/build
*Create and cd into work directory of the form /hive/data/genomes/$db/bed/gencode$GENCODE_VERSION/build
Start a screen.
*Start a screen.
*Copy buildEnv.sh from previous build on this db


== Setting environment variables ==
== Setting environment variables ==

Revision as of 17:26, 26 July 2021

Initialize work directory

  • Create and cd into work directory of the form /hive/data/genomes/$db/bed/gencode$GENCODE_VERSION/build
  • Start a screen.
  • Copy buildEnv.sh from previous build on this db

Setting environment variables

The environment variables used in the build are set in the script buildEnv.sh. All the other scripts assume that this script has been sourced in the current shell.

Extracting Gencode data

Building initial knownGene table

Adding primary reference tables

Building final knownGene core tables