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config.yml
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config.yml
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## SAMPLES AND SAMPLE-SPECIFIC PARAMETERS ==========================================================
# sample id: SRA accessor ids to download raw data. multiple runs per sample will be merged
samples:
Sample10X: SRR9916607
11iv210ng: SRR9916600
11iv22ng: SRR9916599
8iv210ng: SRR9916602
8iv22ng: SRR9916601
8iScreen1: [SRR9916627, SRR9916628, SRR9916629, SRR9916630, SRR9916631, SRR9916632, SRR9916633,
SRR9916634, SRR9916635, SRR9916638, SRR9916637, SRR9916636, SRR9916639, SRR9916640, SRR9916641,
SRR9916642, SRR9916644, SRR9916643, SRR9916647, SRR9916646, SRR9916645, SRR9916650, SRR9916649,
SRR9916648, SRR9916651, SRR9916652, SRR9916653, SRR9916654, SRR9916655, SRR9916656, SRR9916657,
SRR9916658, SRR9916659, SRR9916660, SRR9916661, SRR9916662, SRR9916665, SRR9916664, SRR9916663,
SRR9916666, SRR9916667, SRR9916668]
11iScreen1: [SRR9916669, SRR9916670, SRR9916671, SRR9916672, SRR9916673, SRR9916674, SRR9916675,
SRR9916676, SRR9916677, SRR9916678, SRR9916679, SRR9916680, SRR9916681, SRR9916682, SRR9916683,
SRR9916686, SRR9916685, SRR9916684, SRR9916687, SRR9916688, SRR9916689, SRR9916690, SRR9916691,
SRR9916692, SRR9916693, SRR9916694, SRR9916695, SRR9916696, SRR9916697, SRR9916698, SRR9916701,
SRR9916700, SRR9916699, SRR9916702, SRR9916703, SRR9916704, SRR9916705, SRR9916706, SRR9916707]
WholeTx: [SRR9916615, SRR9916616, SRR9916617, SRR9916618, SRR9916619, SRR9916620, SRR9916621,
SRR9916622, SRR9916623, SRR9916624, SRR9916626, SRR9916625]
TAP1: SRR9916613
TAP2: SRR9916614
W4ea: SRR9916608
T4ea: SRR9916605
TAPtotalBM: [SRR9916609, SRR9916610]
TAPkitBM: [SRR9916611, SRR9916612]
WholeTotalBM: [SRR8181408, SRR8181409, SRR8181410, SRR8181411]
WholeKitBM: [SRR8181412, SRR8181413, SRR8181414, SRR8181415]
wtxmmix: SRR10885108
wtxlung: SRR10885109
tapmix: SRR10885104
taplung: SRR10885105
taphumanmix: SRR10885103
perturbchr8v2: SRR10885110
perturbchr8alt1: SRR10885111
perturbchr8alt2: SRR10951636
perturbL1000: SRR10885106
tapk562deep: SRR10885102
wtxk562deep: SRR10885107
# sample lists for rules handling specific groups of samples
validation: [11iv210ng, 11iv22ng, 8iv210ng, 8iv22ng, Sample10X]
figure1: [tapk562deep, wtxk562deep]
figure2: [TAP1, TAP2, WholeTx, Sample10X]
screen: [8iScreen1, 11iScreen1]
bone_marrow: [TAPtotalBM, TAPkitBM, WholeTotalBM, WholeKitBM]
tapseq_validation: [11iv210ng, 11iv22ng, 8iv210ng, 8iv22ng, Sample10X, wtxmmix, wtxlung, tapmix,
taplung, taphumanmix, perturbchr8v2, perturbchr8alt1, perturbchr8alt2,
perturbL1000, tapk562deep, wtxk562deep, W4ea, T4ea]
# estimated number of cells per sample, for which dge data should be extracted.
cell_numbers:
Sample10X: 8000
11iv210ng: 8500
11iv22ng: 8500
8iv210ng: 7500
8iv22ng: 7500
8iScreen1: 112000
11iScreen1: 120000
WholeTx: 38000
TAP1: 11000
TAP2: 11000
W4ea: 5000
T4ea: 5000
TAPtotalBM: 8000
TAPkitBM: 6000
WholeTotalBM: 2300
WholeKitBM: 2300
wtxmmix: 400
wtxlung: 200
tapmix: 325
taplung: 130
taphumanmix: 400
perturbchr8v2: 2000
perturbchr8alt1: 9000
perturbchr8alt2: 8000
perturbL1000: 9000
tapk562deep: 680
wtxk562deep: 515
# cell and umi barcode base positions in barcode reads for each sample. the first element of the
# array is the cell barcode range, while the second is the UMI barcode range. for screen samples the
# i7 sample barcode was added to the cell barcode, to avoid barcode collisions because multiple 10X
# lanes were multiplexed.
bc_structure:
Sample10X: [1-16, 17-26]
11iv210ng: [1-16, 17-26]
11iv22ng: [1-16, 17-26]
8iv210ng: [1-16, 17-26]
8iv22ng: [1-16, 17-26]
8iScreen1: [1-24, 25-34]
11iScreen1: [1-24, 25-34]
WholeTx: [1-24, 25-34]
TAP1: [1-16, 17-26]
TAP2: [1-16, 17-26]
W4ea: [1-12, 13-20]
T4ea: [1-12, 13-20]
TAPtotalBM: [1-24, 25-34]
TAPkitBM: [1-24, 25-34]
WholeTotalBM: [1-16, 17-26]
WholeKitBM: [1-16, 17-26]
wtxmmix: [1-16, 17-26]
wtxlung: [1-16, 17-26]
tapmix: [1-16, 17-26]
taplung: [1-16, 17-26]
taphumanmix: [1-16, 17-26]
perturbchr8v2: [1-16, 17-26]
perturbchr8alt1: [1-16, 17-26]
perturbchr8alt2: [1-16, 17-26]
perturbL1000: [1-16, 17-26]
tapk562deep: [1-16, 17-26]
wtxk562deep: [1-16, 17-26]
# alignment reference for each sample
align_ref:
Sample10X: data/alignment_references/hg38_genome_ref
11iv210ng: data/alignment_references/hg38_tapseq_ref_validation
11iv22ng: data/alignment_references/hg38_tapseq_ref_validation
8iv210ng: data/alignment_references/hg38_tapseq_ref_validation
8iv22ng: data/alignment_references/hg38_tapseq_ref_validation
8iScreen1: data/alignment_references/hg38_tapseq_ref_chr8_screen
11iScreen1: data/alignment_references/hg38_tapseq_ref_chr11_screen
WholeTx: data/alignment_references/hg38_genome_ref_v2
TAP1: data/alignment_references/hg38_tapseq_ref_validation_v2
TAP2: data/alignment_references/hg38_tapseq_ref_validation_v2
W4ea: data/alignment_references/hg38_genome_ref_dropseq
T4ea: data/alignment_references/hg38_tapseq_ref_dropseq
TAPtotalBM: data/alignment_references/mm10_tapseq_ref_bone_marrow
TAPkitBM: data/alignment_references/mm10_tapseq_ref_bone_marrow
WholeTotalBM: data/alignment_references/mm10_genome_ref
WholeKitBM: data/alignment_references/mm10_genome_ref
wtxmmix: data/alignment_references/mm10_genome_ref
wtxlung: data/alignment_references/mm10_genome_ref
tapmix: data/alignment_references/mm10_tapseq_ref_mix
taplung: data/alignment_references/mm10_tapseq_ref_mix
taphumanmix: data/alignment_references/hg38_tapseq_ref_mix
perturbchr8v2: data/alignment_references/hg38_tapseq_ref_rev
perturbchr8alt1: data/alignment_references/hg38_tapseq_ref_rev
perturbchr8alt2: data/alignment_references/hg38_tapseq_ref_rev
perturbL1000: data/alignment_references/hg38_tapseq_ref_l1000
tapk562deep: data/alignment_references/hg38_tapseq_ref_chr11_noPert
wtxk562deep: data/alignment_references/hg38_genome_ref_mix
# 10x cell barcode whitelist file for each sample
10x_cbc_whitelist:
Sample10X: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
11iv210ng: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
11iv22ng: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
8iv210ng: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
8iv22ng: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
8iScreen1: "meta_data/10x_cell_barcode_whitelists/screen_10x_bc_whitelist_737k_201608.txt.gz"
11iScreen1: "meta_data/10x_cell_barcode_whitelists/screen_10x_bc_whitelist_737k_201608.txt.gz"
WholeTx: "meta_data/10x_cell_barcode_whitelists/wholeTx_10x_bc_whitelist_737k_201608.txt.gz"
TAP1: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
TAP2: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
W4ea: [] # No cell barcode whitelist available for Drop-seq samples
T4ea: [] # No cell barcode whitelist available for Drop-seq samples
TAPtotalBM: "meta_data/10x_cell_barcode_whitelists/bm_tap_10x_bc_whitelist_737k_201608.txt.gz"
TAPkitBM: "meta_data/10x_cell_barcode_whitelists/bm_tap_10x_bc_whitelist_737k_201608.txt.gz"
WholeTotalBM: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
WholeKitBM: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
wtxmmix: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
wtxlung: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
tapmix: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
taplung: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
taphumanmix: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
perturbchr8v2: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
perturbchr8alt1: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
perturbchr8alt2: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
perturbL1000: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
tapk562deep: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
wtxk562deep: "meta_data/10x_cell_barcode_whitelists/10x_bc_whitelist_737k_201608.txt"
# number of minimum molecules per CROP-seq vector to define a cell perturbed for a given vector
perturbation_status:
min_txs:
Sample10X: 4
11iv210ng: 8
11iv22ng: 8
8iv210ng: 8
8iv22ng: 8
8iScreen1: 8
11iScreen1: 8
WholeTx: 8
TAP1: 8
TAP2: 8
W4ea: 2
T4ea: 8
perturbchr8v2: 8
perturbchr8alt1: 8
perturbchr8alt2: 8
perturbL1000: 8
## PARAMETERS FOR INDIVIDUAL RULES =================================================================
# step 1: create alignment reference ---------------------------------------------------------------
download_genome_annot:
hg38:
fasta_url: ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
gtf_url: ftp://ftp.ensembl.org/pub/release-89/gtf/homo_sapiens/Homo_sapiens.GRCh38.89.gtf.gz
mm10:
fasta_url: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/GRCm38.primary_assembly.genome.fa.gz
gtf_url: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz
create_tapseq_ref:
target_genes:
hg38_tapseq_ref_validation: meta_data/target_gene_panels/target_genes_validation.gtf
hg38_tapseq_ref_chr8_screen: meta_data/target_gene_panels/target_genes_chr8_screen.gtf
hg38_tapseq_ref_chr11_screen: meta_data/target_gene_panels/target_genes_chr11_screen.gtf
hg38_tapseq_ref_validation_v2: meta_data/target_gene_panels/target_genes_validation_v2.gtf
hg38_tapseq_ref_validation_v3: meta_data/target_gene_panels/target_genes_validation.gtf
hg38_tapseq_ref_dropseq: meta_data/target_gene_panels/target_genes_validation.gtf
mm10_tapseq_ref_bone_marrow: meta_data/target_gene_panels/target_genes_bone_marrow.gtf
hg38_tapseq_ref_rev: meta_data/target_gene_panels/target_genes_chr8_rev.gtf
mm10_tapseq_ref_mix: meta_data/target_gene_panels/target_genes_mouse_mix.gtf
hg38_tapseq_ref_mix: meta_data/target_gene_panels/target_genes_chr8_rev.gtf
hg38_tapseq_ref_l1000: meta_data/target_gene_panels/target_genes_L1000.gtf.gz
hg38_tapseq_ref_chr11_noPert: meta_data/target_gene_panels/target_genes_chr11_rev.gtf
BSgenome_id:
hg38: BSgenome.Hsapiens.UCSC.hg38
mm10: BSgenome.Mmusculus.UCSC.mm10
create_vector_ref:
vector_fasta:
hg38_genome_ref: meta_data/cropseq_vectors/cropseq_vectors_validation.fasta
hg38_genome_ref_v2: meta_data/cropseq_vectors/cropseq_vectors_validation_v2.fasta
hg38_genome_ref_dropseq: meta_data/cropseq_vectors/cropseq_vectors_dropseq.fasta
hg38_genome_ref_rev: meta_data/cropseq_vectors/cropseq_vectors_rev.fasta
hg38_tapseq_ref_validation: meta_data/cropseq_vectors/cropseq_vectors_validation.fasta
hg38_tapseq_ref_chr8_screen: meta_data/cropseq_vectors/cropseq_vectors_chr8_screen.fasta
hg38_tapseq_ref_chr11_screen: meta_data/cropseq_vectors/cropseq_vectors_chr11_screen.fasta
hg38_tapseq_ref_validation_v2: meta_data/cropseq_vectors/cropseq_vectors_validation_v2.fasta
hg38_tapseq_ref_validation_v3: meta_data/cropseq_vectors/cropseq_vectors_chr8_screen.fasta
hg38_tapseq_ref_dropseq: meta_data/cropseq_vectors/cropseq_vectors_dropseq.fasta
hg38_tapseq_ref_rev: meta_data/cropseq_vectors/cropseq_vectors_rev.fasta
hg38_tapseq_ref_l1000: meta_data/cropseq_vectors/cropseq_vectors_rev.fasta
vector_prefix:
"CROPseq_dCas9_DS_"
create_genomedir:
threads: 5
sjdb_overhang: 57
# step 2: align reads ------------------------------------------------------------------------------
tag_cell_barcodes:
base_quality: 10
num_bases_below_quality: 1
tag_molecule_barcodes:
base_quality: 10
num_bases_below_quality: 1
trim_starting_sequence:
adapter_sequence: AAGCAGTGGTATCAACGCAGAGTGAATGGG
mismatches: 0
num_bases: 5
trim_polyA:
mismatches: 0
num_bases: 6
star_align:
threads: 5
bead_synthesis_error:
min_umis_per_cell: 25
max_num_errors: 1
read_mq: 10
primer_sequence: null
edit_distance: 0
reads_per_cell:
read_quality: 10
# step 3: extract dge data -------------------------------------------------------------------------
umi_observations:
edit_distance: 1
read_mq: 10
min_umi_reads: 0
rare_umi_filter_threshold: 0.0
extract_dge:
tpt_threshold: 0.25
# step 4: analyses ---------------------------------------------------------------------------------
downsample:
reads_per_cell:
11iv210ng: [1000, 1500, 3500]
11iv22ng: [1000, 1500, 3500]
8iv210ng: [1000, 1500, 3500]
8iv22ng: [1000, 1500, 3500]
Sample10X: [1000, 1500, 3500, 5000, 10000, 15000, 20000]
TAP1: [250, 500, 1000, 2000, 2500]
TAP2: [250, 500, 1000, 2000, 2500]
WholeTx: [250, 500, 1000, 2000, 2500, 5000, 10000, 15000]
W4ea: [1000]
T4ea: [1000, 1500, 3500, 5000, 10000, 15000]
TAPtotalBM: [100, 500, 1000, 1500, 2000, 2500, 5000, 5500]
TAPkitBM: [100, 500, 1000, 1500, 2000, 2500, 5000, 5500]
WholeTotalBM: [100, 500, 1000, 1500, 2000, 2500, 5000, 5500, 10000, 20000, 30000, 50000]
WholeKitBM: [100, 500, 1000, 1500, 2000, 2500, 5000, 5500, 10000, 20000, 30000]
wtxmmix: [1000, 1500, 3500, 5000, 10000, 15000, 20000, 40000, 80000, 160000, 320000]
wtxlung: [1000, 1500, 3500, 5000, 10000, 15000, 20000, 40000, 80000, 160000]
tapmix: [1000, 1500, 3500, 5000, 10000, 15000, 20000, 40000, 80000, 160000, 320000]
taplung: [1000, 1500, 3500, 5000, 10000, 15000, 20000, 40000, 80000, 160000, 320000]
taphumanmix: [1000, 1500, 3500, 5000, 10000, 15000, 20000, 40000, 80000, 160000, 250000, 500000]
perturbchr8v2: [500, 1000, 1500, 2000, 5000, 10000, 20000, 40000]
perturbchr8alt1: [500, 1000, 1500, 2000]
perturbchr8alt2: [500, 1000, 1500, 2000, 5000, 10000]
perturbL1000: [1000, 2500, 5000, 7500, 7800]
tapk562deep: [1000, 1500, 3500, 5000, 10000, 15000, 20000, 40000, 80000, 160000, 200000, 300000]
wtxk562deep: [1000, 1500, 3500, 5000, 10000, 15000, 20000, 40000, 80000, 160000, 200000]
# downsample cell type mix TAP-seq samples to the same number of reads on the 150 shared genes
downsampled_150_genes:
reads_per_cell:
taplung: [1000, 1500, 3500, 5000, 10000, 15000, 20000, 40000]
tapmix: [1000, 1500, 3500, 5000, 10000, 15000, 20000, 40000, 80000, 150000]
advanced_dge_downsampling:
target_genes:
WholeTotalBM: "meta_data/target_gene_panels/target_genes_bone_marrow.csv"
WholeKitBM: "meta_data/target_gene_panels/target_genes_bone_marrow.csv"
TAPtotalBM: "meta_data/target_gene_panels/target_genes_bone_marrow.csv"
TAPkitBM: "meta_data/target_gene_panels/target_genes_bone_marrow.csv"
TAP1: "meta_data/target_gene_panels/target_genes_validation_v2.csv"
TAP2: "meta_data/target_gene_panels/target_genes_validation_v2.csv"
WholeTx: "meta_data/target_gene_panels/target_genes_validation_v2.csv"
collapse_perturbations:
targets:
8iScreen1: "meta_data/vector_targets_chr8_screen.csv"
11iScreen1: "meta_data/vector_targets_chr11_screen.csv"
map_enhancers:
remove_lanes:
8iScreen1: []
11iScreen1: ["CATCGACC"]
min_cells:
perEnh: 25
perGRNA: 15
threads: 5
chromatin_analyses:
encode_chip:
H3K27ac: "https://www.encodeproject.org/files/ENCFF779QTH/@@download/ENCFF779QTH.bigWig"
H3K4me1: "https://www.encodeproject.org/files/ENCFF761XBZ/@@download/ENCFF761XBZ.bigWig"
H3K4me3: "https://www.encodeproject.org/files/ENCFF712XRE/@@download/ENCFF712XRE.bigWig"
H3K27me3: "https://www.encodeproject.org/files/ENCFF928NWQ/@@download/ENCFF928NWQ.bigWig"
POLR2A: "https://www.encodeproject.org/files/ENCFF321FZQ/@@download/ENCFF321FZQ.bigWig"
encode_bam:
H3K27ac: "https://www.encodeproject.org/files/ENCFF301TVL/@@download/ENCFF301TVL.bam"
H3K4me1: "https://www.encodeproject.org/files/ENCFF290LQY/@@download/ENCFF290LQY.bam"
H3K4me3: "https://www.encodeproject.org/files/ENCFF611YPB/@@download/ENCFF611YPB.bam"
H3K27me3: "https://www.encodeproject.org/files/ENCFF915XIL/@@download/ENCFF915XIL.bam"
POLR2A: "https://www.encodeproject.org/files/ENCFF438GBD/@@download/ENCFF438GBD.bam"
Dnase-seq: "https://www.encodeproject.org/files/ENCFF538GKX/@@download/ENCFF538GKX.bam"
rao_hic: "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_K562_intrachromosomal_contact_matrices.tar.gz"