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config.yaml
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config.yaml
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#find . $PWD -name '*.narrowPeak.bed' 2>/dev/null
Project: single-cell analysis pipeline
author: Yijia Jiang
date: 20240502
ref: hg38
metasheet: "metasheet.csv"
custom_marker_list: "custom_marker_list.csv"
nCount_RNA_min: 200
nCount_RNA_max: 8000
mito_rate_max: 5
# markers = ["a", "b", c] # can modify function in plot directory
rna_countsamples:
BI54_rna: /mnt/cfce-rcsm/projects/yijiajiang_analysis/20231207_Ellisen_fixed_scRNA/cellranger/Ellisen_BCA/per_sample_outs/BI54/count/sample_filtered_feature_bc_matrix.h5
MGH23039R_rna: /mnt/cfce-rcsm/projects/yijiajiang_analysis/20231207_Ellisen_fixed_scRNA/cellranger/Ellisen_BCA/per_sample_outs/MGH23039R/count/sample_filtered_feature_bc_matrix.h5
BA-1_209_NormR_rna: /mnt/cfce-rcsm/projects/yijiajiang_analysis/20230823_fixed_scRNA_11278/cellranger/BRA_deepseq_twoLib/BCA_usethis/per_sample_outs/BA-1_209_NormR/count/sample_filtered_feature_bc_matrix.h5
BA-8_374_NormL_rna: /mnt/cfce-rcsm/projects/yijiajiang_analysis/20230823_fixed_scRNA_11278/cellranger/BRA_deepseq_twoLib/BCA_usethis/per_sample_outs/BA-8_374_NormL/count/sample_filtered_feature_bc_matrix.h5
# project: scATAC
peak_region_fragments_min: 100
peak_region_fragments_max: 20000
pct_reads_in_peaks: 15
nucleosome_signal: 4
atac_countsamples:
M1_atac: /mnt/cfce-rcsm/projects/yijiajiang_analysis/240226_X202SC24012007-Z01-F002_Sonsoles_scATAC_human/cellranger/M1/outs/filtered_peak_bc_matrix.h5
M2_atac: /mnt/cfce-rcsm/projects/yijiajiang_analysis/240226_X202SC24012007-Z01-F002_Sonsoles_scATAC_human/cellranger/M2/outs/filtered_peak_bc_matrix.h5
B1_7218: /mnt/cfce-rcsm/projects/yijiajiang_analysis/230907_NovaSeq_scATAC/cellranger/B1_7218/outs/filtered_peak_bc_matrix.h5
B2_7157: /mnt/cfce-rcsm/projects/yijiajiang_analysis/230907_NovaSeq_scATAC/cellranger/B2_7157/outs/filtered_peak_bc_matrix.h5
atac_fragments:
M1_atac: /mnt/cfce-rcsm/projects/yijiajiang_analysis/240226_X202SC24012007-Z01-F002_Sonsoles_scATAC_human/cellranger/M1/outs/fragments.tsv.gz
M2_atac: /mnt/cfce-rcsm/projects/yijiajiang_analysis/240226_X202SC24012007-Z01-F002_Sonsoles_scATAC_human/cellranger/M2/outs/fragments.tsv.gz
B1_7218: /mnt/cfce-rcsm/projects/yijiajiang_analysis/230907_NovaSeq_scATAC/cellranger/B1_7218/outs/fragments.tsv.gz
B2_7157: /mnt/cfce-rcsm/projects/yijiajiang_analysis/230907_NovaSeq_scATAC/cellranger/B2_7157/outs/fragments.tsv.gz
atac_peakbed:
M1_atac: /mnt/cfce-rcsm/projects/yijiajiang_analysis/240226_X202SC24012007-Z01-F002_Sonsoles_scATAC_human/cellranger/M1/outs/peaks.bed
M2_atac: /mnt/cfce-rcsm/projects/yijiajiang_analysis/240226_X202SC24012007-Z01-F002_Sonsoles_scATAC_human/cellranger/M2/outs/peaks.bed
B1_7218: /mnt/cfce-rcsm/projects/yijiajiang_analysis/230907_NovaSeq_scATAC/cellranger/B1_7218/outs/peaks.bed
B2_7157: /mnt/cfce-rcsm/projects/yijiajiang_analysis/230907_NovaSeq_scATAC/cellranger/B2_7157/outs/peaks.bed
atac_metadata:
M1_atac: /mnt/cfce-rcsm/projects/yijiajiang_analysis/240226_X202SC24012007-Z01-F002_Sonsoles_scATAC_human/cellranger/M1/outs/singlecell.csv
M2_atac: /mnt/cfce-rcsm/projects/yijiajiang_analysis/240226_X202SC24012007-Z01-F002_Sonsoles_scATAC_human/cellranger/M2/outs/singlecell.csv
B1_7218: /mnt/cfce-rcsm/projects/yijiajiang_analysis/230907_NovaSeq_scATAC/cellranger/B1_7218/outs/singlecell.csv
B2_7157: /mnt/cfce-rcsm/projects/yijiajiang_analysis/230907_NovaSeq_scATAC/cellranger/B2_7157/outs/singlecell.csv
#find . $PWD -name '*.narrowPeak.bed' 2>/dev/null
# Project: scATAnno - annotation
chromsize_file: /mnt/cfce-rcsm/projects/development2/cfce_atac_annotation/BCC_GSE129785/software/QuickATAC/input/hg38.chrom.sizes.txt # data/{assembly}/chrom.sizes.txt
scatac_annotation_references:
PBMC:
spikein: /mnt/cfce-rcsm/projects/development2/cfce_atac_annotation/BCC_GSE129785/software/QuickATAC/input/spikein_fragment_PBMC_narrowPeak.tsv
peak_bed: /mnt/cfce-rcsm/projects/development2/cfce_atac_annotation/BCC_GSE129785/software/QuickATAC/input/PBMC_merged_peaks.narrowPeak.filter.sorted.bed
h5ad: /mnt/cfce-rcsm/homes/yj976/projects/scATAnno/scATAnno-main/data/Reference/PBMC_reference_atlas_final.h5ad
# HealthyAdult:
# spikein: /mnt/cfce-rcsm/projects/development2/cfce_atac_annotation/BCC_GSE129785/software/QuickATAC/input/spikein_fragment_PBMC_narrowPeak.tsv
# peak_bed: /mnt/cfce-rcsm/projects/development2/cfce_atac_annotation/BCC_GSE129785/software/QuickATAC/input/PBMC_merged_peaks.narrowPeak.filter.sorted.bed
# h5ad: /mnt/cfce-rcsm/homes/yj976/projects/scATAnno/scATAnno-main/data/Reference/Healthy_Adult_reference_atlas.h5ad
# TIL:
# spikein: /mnt/cfce-rcsm/projects/development2/cfce_atac_annotation/BCC_GSE129785/software/QuickATAC/input/spikein_fragment_PBMC_narrowPeak.tsv
# peak_bed: /mnt/cfce-rcsm/projects/development2/cfce_atac_annotation/BCC_GSE129785/software/QuickATAC/input/PBMC_merged_peaks.narrowPeak.filter.sorted.bed
# h5ad: PBMC_reference.h5ad
# scatac_annotation_references_spikein:
# PBMC: /mnt/cfce-rcsm/projects/development2/cfce_atac_annotation/BCC_GSE129785/software/QuickATAC/input/spikein_fragment_PBMC_narrowPeak.tsv
# # healthy: path
# # TIL: path
# # PBMC: path
# scatac_annotation_references_bedfile:
# PBMC: /mnt/cfce-rcsm/projects/development2/cfce_atac_annotation/BCC_GSE129785/software/QuickATAC/input/PBMC_merged_peaks.narrowPeak.filter.sorted.bed
# scatac_annotation_references_h5ad:
# PBMC: PBMC_reference.h5ad
# atac_barcodes:
# M1: /mnt/cfce-rcsm/projects/development2/cfce_atac_annotation/BCC_GSE129785/software/QuickATAC/input/snapATAC_PBMC_multiome/ATAC_barcodes.csv