Skip to content

genomes.md

Latest commit

 

History

History
64 lines (54 loc) · 4.2 KB

genomes.md

File metadata and controls

64 lines (54 loc) · 4.2 KB

Reference genomes

The workflow requires a genome reference and annotation to run. All files and settings for a genome are defined in a genome.json file. When launching the workflow, the reference genome is selected by passing the path to a specific genome.json in the --genome parameter.

The genome.json file includes

Field Description Required? Example
name The name of the species / genome-version Required human
bsbolt_index Path to the BSBolt index directory Required (one index required) /PATH/TO/bsbolt.ref
bwa_index Path to the bwa-meth (bwa-mem2) index directory Required (one index required) /PATH/TO/bwa-meth/bwa-mem2.ref
parabricks_index Path to the parabricks (bwa-meth/bwa-mem) index directory Required (one index required) /PATH/TO/bwa-meth/bwa-mem.ref
ref_fasta Name of fasta file within bwa-meth/parabricks index Required (with bwa_index or parabricks_index) hg38.fa
genomeTiles Path to binned genome sorted bed file for CG matrix Optional /PATH/TO/50kbp.bed
genomeTilesCH Path to binned genome sorted bed file for CH matrix Optional /PATH/TO/100kbp.bed
filter_chrs Path to tsv chromosome labels (mito, filter) to filter from deduplicated BAM Required /PATH/TO/filter_chrs.tsv
tssWin Path to bed sorted 200nt windows centered at TSS Required unless runTssEnrich: false /PATH/TO/tss.bed
backgroundWin Path to bed sorted 200nt windows centered at TSS -1kb upstream Required unless runTssEnrich: false /PATH/TO/background.bed
  • All files (bsbolt_index, bins, ...) can be specified either as
    • an absolute path (/path/to/genome)
    • a relative path starting from the location of the genome.json file (genes/bins.bed)
    • a AWS S3 url (s3://path/to/genome)

bwa-meth index (default)

The bwa-meth index needs to be built with bwa-meth version >= 0.2.7 and bwa-mem2 version >= 2.2.1. See the bwa-meth documentation for additional options. An example command would be

bwameth.py index-mem2 {fasta reference}

parabricks index (GPU)

The parabricks index needs to be built with bwa-meth version >= 0.2.7 and bwa-mem version >= 0.7.19. See the bwa-meth documentation for additional options. An example command would be

bwameth.py index {fasta reference}

BSBolt index (legacy)

The BSBolt index needs to be built with BSBolt version >= 1.5.0. See the BSbolt documentation for additional options. An example command would be

bsbolt Index -G {fasta reference} -DB {database output}

Annotation

All genomic non-overlapping bins in the provided genomeTiles and genomeTilesCH bed files are used as features for CG and CH methylation matrix generation.

  • To use bed files with different sized bins (default 50kb) for CG matrix, pass to genomeTiles in the genome.json.
  • To pass a different size bins (default 250kb) for CH matrix, pass to genomeTilesCH in the genome.json.

Pre-built genomes

Pre-built reference genomes are available for download:

Download these to your analysis server, unpack them and then use e.g. --genome /PATH/TO/unpacked/folder/genome.json