config.json

{
  "title": "GSE194214_timecourse",
  "annotation_reference": true,
  "DE_method": "Scran",
  "Number_of_samples": 2,
  "lanes": [ ],
  "DATA_DIR": "/w5home/bmoore/scRNAseq/LiFangChu/public_data/GSE194214/",
    "fastq_alignment": {
        "SAMPLE_1": {
            "NAME": "Day1",
            "species": "human",
            "NUM_LANES": 2,
            "cDNA_LANE1": "/data/SRR17712089_2.fastq.gz",
            "BARCODE_LANE1": "/data/SRR17712089_1.fastq.gz",
            "cDNA_LANE2": "/data/SRR17712090_2.fastq.gz",
            "BARCODE_LANE2": "/data/SRR17712090_1.fastq.gz",
            "CHEMISTRY_VERSION": "V3",
            "SOLO_TYPE": "CB_UMI_Simple",
            "SOLO_MULTI_MAPPERS": "EM",
            "READ_FILES_COMMAND": "zcat",
            "SOLO_UMI_DEDUP": "1MM_CR",
            "RUN_THREAD_N": 8,
            "isBarcodeFollowedbyReads": false,
            "clip5pNbases": "0 91"
        },
        "SAMPLE_2": {
            "NAME": "Day2",
            "species": "human",
            "NUM_LANES": 2,
            "cDNA_LANE1": "/data/SRR17712087_2.fastq.gz",
            "BARCODE_LANE1": "/data/SRR17712087_1.fastq.gz",
            "cDNA_LANE2": "/data/SRR17712088_2.fastq.gz",
            "BARCODE_LANE2": "/data/SRR17712088_1.fastq.gz",
            "CHEMISTRY_VERSION": "V3",
            "SOLO_TYPE": "CB_UMI_Simple",
            "SOLO_MULTI_MAPPERS": "EM",
            "READ_FILES_COMMAND": "zcat",
            "SOLO_UMI_DEDUP": "1MM_CR",
            "RUN_THREAD_N": 8,
            "isBarcodeFollowedbyReads": false,
            "clip5pNbases": "0 91"
        }
    },
    "prep_seurat_and_soupX": {
        "dims": 30,
        "umap.method": "umap-learn",
        "tfidfMin": 1,
        "min.cells": 3
    },
    "filter_cells": {
        "lower.nFeature": 200,
        "upper.nFeature": 15000,
        "max.percent.mt": 20
    },
    "ortholog_subset": {
        "ortholog_file": "../metadata/Human_Pig_Biomart_Filtered_mod.txt",
        "ref_species": "human"
    },
    "normalize_data": {
        "min_size": 100,
        "min_mean": 0.1,
        "feature": "ECHS1"
    },
    "feature_selection": {
        "n_features": 2000,
        "analysis_type": "Scry"
    },
    "scale_data": {
        "vars.2.regress": "cell.cycle",
        "marker.path.s": "../cell_cycle_vignette/cell_cycle_orthologs_s.genes.txt",
        "marker.path.g2m": "../cell_cycle_vignette/cell_cycle_orthologs_g2m.genes.txt"
    },
    "run_and_visualize_pca": {
        "top_n_dims": 2,
        "heatmap_dims": 15,
        "num_cells": 500,
        "dims": 20,
        "num.replicate": 100
    },
    "run_umap": {
        "dims_umap": 20,
        "umap.method": "umap-learn",
        "umap.red": "harmony"
    },
    "perform_batch_correction": {
        "dims.use": 20,
        "max_iter": 50
    },
    "perform_clustering": {
        "reduction": "harmony",
        "resolution": 0.5,
        "algorithm": "leiden",
        "dims_snn": 10
    },
    "find_differentially_expressed_features": {
        "min_pct": 0.25,
        "logfc_threshold": 0.25,
        "top_n": 11
    },
    "get_metadata": {
        "metadata_file_ref": "../metadata/Reh_cca_org_205_metadata.txt",
        "metadata_file_query": "../metadata/gammS2_manual_annot_metadata_c0.5.txt",
        "metadata_subset1": "NA",
        "metadata_subset2": "NA"
    },
    "score_and_plot_markers": {
        "top_n_markers": 100,
        "known_markers": "TRUE",
        "known_markers_path": "../known_marker_lists/JackChu_markers.txt",
        "cluster_type": "seurat_clusters",
        "pairwise": "FALSE",
        "logFC_thresh": 0.5,
        "auc_thresh": 0.5
    },
    "process_known_markers": {
        "annot_type": "manual",
        "n_rank": 10
    },
    "transfer_anchors": {
        "reduc.type": "cca"
    }
}