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455 | {
"server": "https://platform.genexplain.com",
"user": "someuser@email.io",
"password": "12345",
"reconnect": true,
"replaceStrings": [
["$SPECIES", "Human (Homo sapiens)"],
["$GENOME_MAPPING", "hg18->hg38"],
["$ENSEMBL_104_SELECTOR", "Ensembl 104.38 Human (hg38)"],
["$MEALR_TRANSFAC_PROFILE", "databases/TRANSFAC(R) 2022.1/Data/profiles/vertebrate_human_p0.05_non3d"],
["$GRN_TRANSFAC_PROFILE", "databases/TRANSFAC(R) 2022.1/Data/profiles/vertebrate_human_p0.001_non3d"],
["$BED_PATH_ALL", "$FOLDER_PATH/GSM614003_jurkat.tal1"],
["$MAPPED_GENES_GO_PATH", "$MAPPED_GENE_PATH_ALL GO"],
["$MAPPED_GENES_REACTOME_PATH", "$MAPPED_GENE_PATH_ALL Reactome"],
["$MAPPED_GENES_HUMANPSD_PATH", "$MAPPED_GENE_PATH_ALL Human disease biomarkers"],
["$MAPPED_GENE_PATH_ALL", "$MAPPED_PATH_ALL Genes"],
["$MEALR_BACKGROUND_PATH", "$MAPPED_PATH_ALL random 1000"],
["$MAPPED_PATH_ALL", "$FOLDER_PATH/jurkat_chipseq_hg38"],
["$UNMAPPED_PATH_ALL", "$FOLDER_PATH/jurkat_chipseq_hg38_unmapped"],
["$BED_PATH_SAMPLE", "$FOLDER_PATH/GSM614003_jurkat.tal1_1000"],
["$MEALR_TOP_GENE_PATH", "$MEALR_TOP_PATH Genes"],
["$GRN_FACTOR_PATH", "$MEALR_VENN_PATH/Rows present in both tables"],
["$GRN_MATCH_PATH", "$GRN_PWM_PROFILE Match"],
["$TAL1_MATCH_PATH", "$GRN_PWM_PROFILE TAL1 Match"],
["$GRN_PWM_PROFILE", "$GRN_PWM_PATH profile"],
["$GRN_PWM_PATH", "$MEALR_OUTPUT_PATH/grn_pwms"],
["$TAL1_TRACK_PATH", "$TAL1_GENE_PATH promoter"],
["$TAL1_GENE_PATH", "$MEALR_OUTPUT_PATH/tal1"],
["$MEALR_VENN_PATH", "$MEALR_TOP_PATH Venn"],
["$MEALR_TOP_PATH", "$MEALR_MOTIF_PATH Top 50"],
["$MEALR_MOTIF_PATH", "$MEALR_OUTPUT_PATH/MEALR_positive_coefficients"],
["$MEALR_OUTPUT_PATH", "$MAPPED_PATH_SAMPLE MEALR"],
["$MAPPED_PATH_SAMPLE", "$FOLDER_PATH/jurkat_chipseq_hg38_1000"],
["$UNMAPPED_PATH_SAMPLE", "$FOLDER_PATH/jurkat_chipseq_hg38_1000_unmapped"],
["$FOLDER_PATH", "$PARENT_FOLDER$/$FOLDER_NAME$"],
["$PARENT_FOLDER$", "data/Projects/api2022_tutorial/Data"],
["$FOLDER_NAME$", "chipseq_analysis_workflow_json"],
["$CHIPSEQ_BED_ALL", "../data/GSM614003_jurkat.tal1.bed"],
["$CHIPSEQ_BED_SAMPLE", "../data/GSM614003_jurkat.tal1_1000.bed"],
["$WAIT_SCRIPT", "waitns.sh"],
["$PWM_ID_SCRIPT", "chipseq_analysis_grn_pwms.py"],
["$TAL1_GENE_SCRIPT", "chipseq_analysis_tal1.py"]
],
"tasks": [
{
"do": "createFolder",
"showOutput": true,
"path": "$PARENT_FOLDER$",
"name": "$FOLDER_NAME$",
"comment": "Prepare folder for analysis data and results"
},
{
"do": "imPort",
"file": "$CHIPSEQ_BED_ALL",
"path": "$FOLDER_PATH",
"importer": "BED format (*.bed)",
"verbose": true,
"parameters": {
"dbSelector": "Ensembl 52.36n Human (hg18)"
},
"comment": "Step 1.1 Import the BED file with TAL1-bound regions into the destination folder"
},
{
"do": "external",
"showOutput": true,
"bin": "sh",
"params": ["$WAIT_SCRIPT"],
"comment": "Run external script to allow server process to finish before using imported data"
},
{
"do": "analyze",
"method": "liftOver1",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"input": "$BED_PATH_ALL",
"mapping": "$GENOME_MAPPING",
"minMatch": 0.95,
"out_file1": "$MAPPED_PATH_ALL",
"out_file2": "$UNMAPPED_PATH_ALL"
},
"comment": "Step 1.2 Run Liftover to map hg18 coordinates to hg38"
},
{
"do": "analyze",
"method": "Track to gene set",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"sourcePaths": ["$MAPPED_PATH_ALL"],
"species": "$SPECIES",
"from": -5000,
"to": 2000,
"destPath": "$MAPPED_GENE_PATH_ALL"
},
"comment": "Step 2. Run 'Track to gene set' tool to map genomic coordinates to genes"
},
{
"do": "analyze",
"method": "Functional classification",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"sourcePath": "$MAPPED_GENE_PATH_ALL",
"species": "$SPECIES",
"bioHub": "Full gene ontology classification",
"minHits": 1,
"pvalueThreshold": 1,
"outputTable": "$MAPPED_GENES_GO_PATH"
},
"comment": "Step 3.1 Enrichment of genes associated with Gene Ontology terms using 'Functional classification'"
},
{
"do": "export",
"file": "functional_classification_result_GO.tsv",
"path": "$MAPPED_GENES_GO_PATH",
"exporter": "Tab-separated text (*.txt)",
"parameters": {},
"comment": "Step 3.2 Export analysis results to local file"
},
{
"do": "analyze",
"method": "Functional classification",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"sourcePath": "$MAPPED_GENE_PATH_ALL",
"species": "$SPECIES",
"bioHub": "Reactome pathways (74)",
"minHits": 1,
"pvalueThreshold": 1,
"outputTable": "$MAPPED_GENES_REACTOME_PATH"
},
"comment": "Step 3.3 Enrichment of genes associated with Reactome pathways using 'Functional classification'"
},
{
"do": "export",
"file": "functional_classification_result_Reactome.tsv",
"path": "$MAPPED_GENES_REACTOME_PATH",
"exporter": "Tab-separated text (*.txt)",
"parameters": {},
"comment": "Step 3.4 Export analysis results to local file"
},
{
"do": "analyze",
"method": "Functional classification",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"sourcePath": "$MAPPED_GENE_PATH_ALL",
"species": "$SPECIES",
"bioHub": "HumanPSD(TM) disease (2022.1)",
"minHits": 1,
"pvalueThreshold": 1,
"outputTable": "$MAPPED_GENES_HUMANPSD_PATH"
},
"comment": "Step 3.5 Enrichment of biomarkers of human diseases annotated in the HumanPSD knowledgebase"
},
{
"do": "export",
"file": "functional_classification_result_HumanPSD.tsv",
"path": "$MAPPED_GENES_HUMANPSD_PATH",
"exporter": "Tab-separated text (*.txt)",
"parameters": {},
"comment": "Step 3.6 Export analysis results to local file"
},
{
"do": "analyze",
"method": "Create random track",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"inputTrackPath": "$MAPPED_PATH_ALL",
"dbSelector": "$ENSEMBL_104_SELECTOR",
"species": "$SPECIES",
"standardChromosomes": true,
"seqNumber": 1000,
"seqLength": 0,
"from": 0,
"to": 0,
"withOverlap": false,
"randomShift": false,
"outputTrackPath": "$MEALR_BACKGROUND_PATH",
"randSeed": 123
},
"comment": "Step 4. Create random track not overlapping with TAL1-bound regions"
},
{
"do": "imPort",
"file": "$CHIPSEQ_BED_SAMPLE",
"path": "$FOLDER_PATH",
"importer": "BED format (*.bed)",
"verbose": true,
"parameters": {
"dbSelector": "Ensembl 52.36n Human (hg18)"
},
"comment": "Step 5.1 Import sampled TAL1 ChIP-seq sites"
},
{
"do": "external",
"showOutput": true,
"bin": "sh",
"params": ["$WAIT_SCRIPT"],
"comment": "Run external script to allow server process to finish before using imported data"
},
{
"do": "analyze",
"method": "liftOver1",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"input": "$BED_PATH_SAMPLE",
"mapping": "$GENOME_MAPPING",
"minMatch": 0.95,
"out_file1": "$MAPPED_PATH_SAMPLE",
"out_file2": "$UNMAPPED_PATH_SAMPLE"
},
"comment": "Step 5.2 Map coordinates from hg18 to hg38"
},
{
"do": "analyze",
"method": "MEALR (tracks)",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"yesSetPath": "$MAPPED_PATH_SAMPLE",
"noSetPath": "$MEALR_BACKGROUND_PATH",
"dbSelector": "$ENSEMBL_104_SELECTOR",
"profilePath": "$MEALR_TRANSFAC_PROFILE",
"maxPosCoef": 150,
"maxComplexity": 0.5,
"complexityInc": 0.02,
"maxUnimproved": 20,
"scoresWithNoSet": false,
"output": "$MEALR_OUTPUT_PATH"
},
"comment": "Step 6. Analyze target and background genomic regions using MEALR to find important PWMs"
},
{
"do": "analyze",
"method": "Select top rows",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"inputTable": "$MEALR_MOTIF_PATH",
"column": "Coefficient",
"types": ["Top"],
"topPercent": 100.0,
"topCount": 50,
"topMinCount": 50,
"topTable": "$MEALR_TOP_PATH"
},
"comment": "Step 7.1 Extract top 50 PWMs ranked by logistic regression coefficient"
},
{
"do": "analyze",
"method": "Matrices to molecules",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"sitesCollection": "$MEALR_TOP_PATH",
"siteModelsCollection": "$MEALR_TRANSFAC_PROFILE",
"species": "$SPECIES",
"targetType": "Genes: Ensembl",
"outputTable": "$MEALR_TOP_GENE_PATH"
},
"comment": "Step 7.2 Convert PWMs to factor genes"
},
{
"do": "analyze",
"method": "Venn diagrams",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"table1Path": "$MAPPED_GENE_PATH_ALL",
"table1Name": "Genes near TAL1 sites",
"table2Path": "$MEALR_TOP_GENE_PATH",
"table2Name": "MEALR transcription factors",
"simple": true,
"output": "$MEALR_VENN_PATH"
},
"comment": "Step 8 Intersect factors identified by MEALR and genes with nearby TAL1 ChIP-seq sites"
},
{
"do": "get",
"table": "$GRN_FACTOR_PATH",
"toFile": "grn_factors.json",
"comment": "Step 9.1 Download table with potential GRN factors to local file"
},
{
"do": "external",
"bin": "python3",
"params": [
"$PWM_ID_SCRIPT"
],
"comment": "Step 9.2 Run external script to create PWM table"
},
{
"do": "imPort",
"file": "grn_pwms.tsv",
"path": "$MEALR_OUTPUT_PATH",
"importer": "Tabular (*.txt, *.xls, *.tab, etc.)",
"parameters": {
"columnForID": "PWM",
"tableType": "Matrices: TRANSFAC",
"species": "Human (Homo sapiens)"
},
"comment": "Step 9.3 Import PWM table created by external script"
},
{
"do": "external",
"showOutput": true,
"bin": "sh",
"params": ["$WAIT_SCRIPT"],
"comment": "Run external script to allow server process to finish before using imported data"
},
{
"do": "analyze",
"method": "Create profile from site model table",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"table": "$GRN_PWM_PATH",
"profile": "$GRN_TRANSFAC_PROFILE",
"outputProfile": "$GRN_PWM_PROFILE"
},
"comment": "Step 9.4 Create Match(TM) profile for PWMs of potential GRN factors"
},
{
"do": "analyze",
"method": "TRANSFAC(R) Match(TM) for tracks",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"sequencePath": "$MAPPED_PATH_ALL",
"dbSelector": "$ENSEMBL_104_SELECTOR",
"profilePath": "$GRN_PWM_PROFILE",
"withoutDuplicates": true,
"ignoreCore": true,
"output": "$GRN_MATCH_PATH"
},
"comment": "Step 9.5 Predict binding sites of GRN factors in TAL1-bound regions"
},
{
"do": "external",
"bin": "python3",
"params": [
"$TAL1_GENE_SCRIPT"
],
"comment": "Step 10.1 Run external script to prepare TAL1 gene table"
},
{
"do": "imPort",
"file": "tal1.tsv",
"path": "$MEALR_OUTPUT_PATH",
"importer": "Tabular (*.txt, *.xls, *.tab, etc.)",
"parameters": {
"columnForID": "ID",
"tableType": "Genes: Ensembl",
"species": "Human (Homo sapiens)"
},
"comment": "Step 10.2 Import TAL1 gene table"
},
{
"do": "external",
"showOutput": true,
"bin": "sh",
"params": ["$WAIT_SCRIPT"],
"comment": "Run external script to allow server process to finish before using imported data"
},
{
"do": "analyze",
"method": "Gene set to track",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"sourcePath": "$TAL1_GENE_PATH",
"species": "$SPECIES",
"from": 2000,
"to": 1000,
"destPath": "$TAL1_TRACK_PATH"
},
"comment": "Step 10.3 Create track of genomic region around TAL1 TSS (promoter)"
},
{
"do": "analyze",
"method": "TRANSFAC(R) Match(TM) for tracks",
"workflow": false,
"wait": true,
"progress": true,
"parameters": {
"sequencePath": "$TAL1_TRACK_PATH",
"dbSelector": "$ENSEMBL_104_SELECTOR",
"profilePath": "$GRN_PWM_PROFILE",
"withoutDuplicates": true,
"ignoreCore": true,
"output": "$TAL1_MATCH_PATH"
},
"comment": "Step 10.4 Predict binding sites of GRN factors in TAL1 promoter"
},
{
"do": "export",
"file": "TAL1_grn_pwm_sites.bed",
"path": "$TAL1_MATCH_PATH",
"exporter": "BED format (*.bed)",
"parameters": {},
"comment": "Step 10.5 Export genomic locations of predicted sites for GRN factors around TAL1 TSS"
}
]
}
|