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Reference genomes

The workflow requires a set of genome reference files and settings to run. All files and settings for a genome are defined in a genome.json file. When launching the workflow, a reference genome is chosen by passing the path to a specific genome.json in the genome parameter (in params.yml or --genome)

The genome.json file includes

Field Description Required? Example
name The name of the species / genome-version Required human
bowtie_index Path to the bowtie2 index directory and prefix Required bowtie2/GRCh38
gtf Path to the gene annotation Optional; used for TSS / promoter analysis filteredGTF/GRCh38_transcripts.gtf
macs_genome Name of the genome for the MACS peak-caller optional; used to adjust MACS parameters "hs"
speciesName Name of the species for OrgDb optional; used for ArchR analysis Homo sapiens
archrAlias Name of the genome for [ArchR] (https://www.archrproject.com/bookdown/getting-set-up.html) optional; used for ArchR analysis hg38
annotationConvention For non-standard ArchR genomes optional; used for ArchR analysis ENSEMBL
  • All files (bowtie_index, gtf, ...) can be either
    • An absolute path (/path/to/genome)
    • A relative path starting from the location of the genome.json file (genes/filtered.gtf)
    • A AWS S3 url (s3://path/to/genome)
  • The ArchR settings are only needed for downstream analysis (clustering etc.) and optional

Pre-built genomes

Pre-build reference genomes for human and mouse are available for download:

Download these to your analysis server, unpack them and then use e.g. --genome path/to/genomes/grch38/grch38.json

GTF Filtering

The workflow includes a tool to pre-filter a GTF to a subset of features (genes / transcripts). This filtered GTF can then be used for analysis:

  1. Navigate to the directory with your initial .gtf file.
  2. Create a gtfFilter.json by which to filter your GTF (example)
  3. Install script dependency: pip install pybedtools
  4. Use script to filter your gtf:

ScaleTagToolkit/bin/filter_gtf.py -gtf <path/to/genes.gtf> -j <pathToFilterJson> -o <path/to/filtered.gtf>

  1. Replace the gtf field of the genome.json with the your newly created filtered.gtf