dbs.md

Adding databases

Databases are sorted into different categories:

• c2g: CRE to gene databases (e.g. eQTL studies)
• cre: CRE annotation (e.g. ENCODE)
• gen: general genome annotations (e.g. lambert, ENSMBL)
• gst: Gene set databases (e.g. REACTOME)
• ont: Ontology databases
• prt: TF perturbation databases (e.g. KnockTF)
• tfb: TF binding databases (e.g. ChIP-Atlas)
• tfm: TF marker databases (e.g. TF-Marker)
• tfp: TF-TF interaction databases (e.g. IntAct)
• tss: TSS databases (e.g. ENSMBL)

A url where to download the database should be provided in the config/config.yaml file.

# Databases
dbs:
    hg38:
        gen:
            ...
        prt:
            ...
        gst:
            ...
            newdatabase: 'https:// ...'
    mm10:
        ...

Note that databases are divided by organism.

Rules for each of these categories can be found in workflow/rules/dbs/. New databases should be added to their corresponding rule file. If a database does not fit any of these categories, a new rule file can be created.

Here is an example of a rule for CRE:

rule cre_encode:
    threads: 1
    output: 'dbs/hg38/cre/encode/encode.bed'
    params:
        url=config['dbs']['hg38']['cre']['encode']
    shell:
        """
        ...
        """

Rules should follow this naming convetion: {dbtype_dbname}, in this case cre_encode. The output should be stored using this path format: dbs/{organism}/{dbtype}/{dbname}/{dbname}.bed When possible use .bed format, else csv.