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build_genome_database.md

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How to build genome database

  1. Install Conda. Skip this if you already have equivalent Conda alternatives (Anaconda Python). Download and run the installer. Agree to the license term by typing yes. It will ask you about the installation location. On Stanford clusters (Sherlock and SCG4), we recommend to install it outside of your $HOME directory since its filesystem is slow and has very limited space. At the end of the installation, choose yes to add Miniconda's binary to $PATH in your BASH startup script.

    $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh

  2. Install Conda dependencies.

    $ bash conda/uninstall_dependencies.sh  # to remove any existing pipeline env
$ bash conda/install_dependencies.sh

  3. Choose [GENOME] from hg19, hg38, mm9 and mm10 and specify a destination directory. This will take several hours. We recommend not to run this installer on a login node of your cluster. It will take >8GB memory and >2h time.

    $ bash conda/build_genome_data.sh [GENOME] [DESTINATION_DIR]

  4. Find a TSV file on the destination directory and use it for "atac.genome_tsv" in your input JSON.

How to build genome database for your own genome

  1. You can build your own genome database if your reference genome has one of the following file types.

    • .fasta.gz
    • .fa.gz
    • .fasta.bz2
    • .fa.gz2
    • .2bit

  2. Get a URL for your reference genome. You may need to upload it to somewhere on the internet.

  3. Get a URL for a gzipped blacklist BED file for your genome. If you don't have one then skip this step. An example blacklist for hg38 is here.

  4. Find the following lines in conda/build_genome_data.sh and modify it. Give a good name [YOUR_OWN_GENOME] for your genome.

    ...

elif [[ $GENOME == "YOUR_OWN_GENOME" ]]; then
  REF_FA="URL_FOR_YOUR_FASTA_OR_2BIT"
  BLACKLIST= # leave it empty if you don't have it

...

  5. Specify a destination directory for your genome database and run the installer. This will take several hours.

    $ bash conda/build_genome_data.sh [YOUR_OWN_GENOME] [DESTINATION_DIR]

  6. Find a TSV file in the destination directory and use it for "atac.genome_tsv" in your input JSON.