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ref.yaml
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ref.yaml
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#REF.yaml - File to contain paths to static reference files that Chips requires
# for its analysis.
# NOTE: these are already pre-filled for hg19 and mm9 (if you use the publicly
# available files found here: <link to chips static references)
# NOTE: organized by assemblies
#
# !VERY IMPORTANT: you can OVERRIDE any of these values in config.yaml!
GDC_hg38:
bwa_index: ./ref_files/GDC_hg38/bwa_indices/GDC_hg38/GRCh38.d1.vd1.CIDC.fa
geneTable: ./ref_files/GDC_hg38/GDC_hg38.refGene
geneBed: ./ref_files/GDC_hg38/GDC_hg38_refGene.bed
conservation: ./ref_files/GDC_hg38/conservation/hg38.phastCons100way.bw
DHS: ./ref_files/GDC_hg38/regions/hg38_cCREs.bed
exons: ./ref_files/GDC_hg38/regions/exon.bed
promoters: ./ref_files/GDC_hg38/regions/promoter.bed
velcro_regions:
chrom_lens: ./ref_files/GDC_hg38/regions/chromInfo_hg38.txt
#MACS2 genome_size param: hs = 2.7e9, mm = 1.87e9, ce = 9e7, dm = 1.2e8
genome_size: "2.7e9"
#LEN: SHOULD MAYBE change to motif_genome
motif_path: hg38
hg38:
bwa_index: ./ref_files/hg38/bwa_indices/hg38/hg38.fa
geneTable: ./ref_files/hg38/hg38.refGene
geneBed: ./ref_files/hg38/hg38_refGene.bed
conservation: ./ref_files/hg38/conservation/hg38.phastCons100way.bw
DHS: ./ref_files/hg38/regions/hg38_cCREs.bed
exons: ./ref_files/hg38/regions/exon.bed
promoters: ./ref_files/hg38/regions/promoter.bed
velcro_regions:
chrom_lens: ./ref_files/hg38/regions/chromInfo_hg38.txt
#MACS2 genome_size param: hs = 2.7e9, mm = 1.87e9, ce = 9e7, dm = 1.2e8
genome_size: "2.7e9"
#LEN: SHOULD MAYBE change to motif_genome
motif_path: hg38
hg19:
bwa_index: ./ref_files/hg19/bwa_indices/hg19/hg19.fa
geneTable: ./ref_files/hg19/hg19.refGene
geneBed: ./ref_files/hg19/hg19_refGene.bed
conservation: ./ref_files/hg19/conservation/hg19.100way.phastCons.bw
DHS: ./ref_files/hg19/regions/DHS_hg19.bed
exons: ./ref_files/hg19/regions/exon.bed
promoters: ./ref_files/hg19/regions/promoter.bed
velcro_regions: ./ref_files/hg19/regions/wgEncodeHg19ConsensusSignalArtifactRegions.bed
chrom_lens: ./ref_files/hg19/regions/hg19.len
#MACS2 genome_size param: hs = 2.7e9, mm = 1.87e9, ce = 9e7, dm = 1.2e8
genome_size: "2.7e9"
#LEN: SHOULD MAYBE change to motif_genome
motif_path: hg19
mm10:
bwa_index: ./ref_files/mm10/bwa_indices/mm10.fa
geneTable: ./ref_files/mm10/mm10.refGene
geneBed: ./ref_files/mm10/mm10_refGene.bed
conservation: ./ref_files/mm10/conservation/mm10.60way.phastCons.bw
DHS: ./ref_files/mm10/regions/mm10.DHS.bed
exons: ./ref_files/mm10/regions/mm10.exon.bed
promoters: ./ref_files/mm10/regions/mm10.promoter.bed
velcro_regions:
chrom_lens: ./ref_files/mm10/regions/mm10.len
#MACS2 genome_size param: hs = 2.7e9, mm = 1.87e9, ce = 9e7, dm = 1.2e8
genome_size: "1.87e9"
#LEN: SHOULD MAYBE change to motif_genome
motif_path: mm10
mm9:
bwa_index: ./ref_files/mm9/bwa_indices/mm9/mm9.fa
geneTable: ./ref_files/mm9/mm9.refGene
geneBed: ./ref_files/mm9/mm9_refGene.bed
conservation: ./ref_files/mm9/conservation/mm9.phaston.30way.bw
DHS: ./ref_files/mm9/regions/DHS_mm9.bed
exons: ./ref_files/mm9/regions/mm9_exon.bed
promoters: ./ref_files/mm9/regions/mm9_promoter.bed
velcro_regions:
chrom_lens: ./ref_files/mm9/regions/mm9.len
#MACS2 genome_size param: hs = 2.7e9, mm = 1.87e9, ce = 9e7, dm = 1.2e8
genome_size: "1.87e9"
#LEN: SHOULD MAYBE change to motif_genome
motif_path: mm9
rn5:
bwa_index: ./ref_files/rn5/bwa_indices/rn5/rn5.fa
geneTable: ./ref_files/rn5/rn5.refGene
conservation: ./ref_files/rn5/conservation/rn5/vertebrate
DHS:
exons: ./ref_files/rn5/regions/exon.bed
promoters: ./ref_files/rn5/regions/promoter.bed
velcro_regions:
chrom_lens: ./ref_files/rn5/regions/rn5.len
#MACS2 genome_size param: hs = 2.7e9, mm = 1.87e9, ce = 9e7, dm = 1.2e8
#NOTE: as this value is not provided by MACS2, we are using the Ungapped
#Length found here:
#https://www.ncbi.nlm.nih.gov/assembly/GCF_000001895.4/#/st
genome_size: "2.57e9"
#LEN: SHOULD MAYBE change to motif_genome
motif_path: rn5
rn6:
bwa_index: ./ref_files/rn6/bwa_indices/rn6/rn6.fa
geneTable: ./ref_files/rn6/rn6.refGene
conservation: ./ref_files/rn6/conservation/rn6/vertebrate
DHS:
exons: ./ref_files/rn6/regions/exon.bed
promoters: ./ref_files/rn6/regions/promoter.bed
velcro_regions:
chrom_lens: ./ref_files/rn6/regions/rn6.len
#MACS2 genome_size param: hs = 2.7e9, mm = 1.87e9, ce = 9e7, dm = 1.2e8
#NOTE: as this value is not provided by MACS2, we are using the Ungapped
#Length found here:
#https://www.ncbi.nlm.nih.gov/assembly/GCF_000001895.4/#/st
genome_size: "2.57e9"
#LEN: SHOULD MAYBE change to motif_genome
motif_path: rn6
#NOTE: optional contamination panel to check sample contamination against
#Each element should be a path to the INDEX for the aligner you want to use
#The name of the file will be used in the table report,
#e.g. /some/path/to/BWA/e_coli.fasta will be reported as "e_coli"
contamination_panel:
#- /some/path/to/BWA_index/
#- /some/path/to/BWA_index/
#- ./ref_files/contam_panel/GDC_hg38/GRCh38.d1.vd1.CIDC.fa
#- ./ref_files/contam_panel/hg38/hg38.fa
#- ./ref_files/contam_panel/hg19/hg19.fa
#- ./ref_files/contam_panel/mm9/mm9.fa
- ./ref_files/contam_panel/dm3/dm3.fa
- ./ref_files/contam_panel/S_cerevisiae/S_cerevisiae.fa
- ./ref_files/contam_panel/e_coli/e_coli.fasta
- ./ref_files/contam_panel/mycoplasma/GCF_000018785.1_ASM1878v1/myco_PG-8A.fna
- ./ref_files/contam_panel/mycoplasma/GCF_000085865.1_ASM8586v1/myco_ATCC23114.fna
- ./ref_files/contam_panel/mycoplasma/GCF_000186005.1_ASM18600v1/myco_m64.fna
- ./ref_files/contam_panel/mycoplasma/GCF_000313635.1_ASM31363v1/myco_SK76.fna
- ./ref_files/contam_panel/mycoplasma/GCF_000420105.1_ASM42010v1/myco_ATCC23714.fna
- ./ref_files/contam_panel/mycoplasma/GCF_000485555.1_ASM48555v1/myco_ATCC23064.fna
- ./ref_files/contam_panel/mycoplasma/GCF_001547975.1_ASM154797v1/myco_HAZ145_1.fna
- ./ref_files/contam_panel/mycoplasma/GCF_000027345.1_ASM2734v1/myco_ATCC29342.fna
- ./ref_files/contam_panel/mycoplasma/GCF_000092585.1_ASM9258v1/myco_R.fna
- ./ref_files/contam_panel/mycoplasma/GCF_000969765.1_ASM96976v1/myco_WVU1853.fna