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config_cls3test.json
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config_cls3test.json
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{
"GENOMESDIR": "genomes/",
"produceStatPlots": true,
"produceTrackHub": true,
"produceHtmlStatsTable": true,
"capDesignToGenome": {
"HpreCap": "hg38",
"Hv3": "hg38",
"MpreCap": "mm10",
"Mv2": "mm10"
},
"capDesignToTargetsGff": {
"Hv3": "targets/Hv3_primary_targets.exons.reduced.gene_type.segments.gtf",
"Mv2": "targets/Mv2_primary_targets.exons.reduced.gene_type.segments.gtf"
},
"capDesignToCapDesign": {
"HpreCap": "Hv3",
"MpreCap": "Mv2",
"Hv3": "Hv3",
"Mv2": "Mv2"
},
"sampleRepGroupBy": [
"seqPlatform",
"libraryPrep",
"species",
"captureDesign",
"sizeFrac",
"tissue",
"cellFrac",
"reverse_transcriptase"
],
"CAPTURE": true,
"SAMPLE_ANNOT": "annotations/samples/sample_annotations.tsv",
"genomeToAnnotGtf": {
"hg38": "annotations/hs.gencode24+SIRVS.gff",
"mm10": "annotations/mm.gencodeM7+SIRVS.gff"
},
"USE_MATCHED_ILLUMINA": true,
"PROJECT_NAME": "CLS3test",
"PROJECT_LONG_NAME": "GENCODE CLS Phase 3 test",
"PROJECT_CONTACT_EMAIL": "julien.lagarde@crg.eu",
"TRACK_HUB_BASE_URL": "https://public-docs.crg.es/rguigo/Data/jlagarde/gencode/trackHubs/CLS3test/",
"genomeToCAGEpeaks": {
"hg38": "annotations/cage/hg38_fair+new_CAGE_peaks_phase1and2.bed",
"mm10": "annotations/cage/mm10_fair+new_CAGE_peaks_phase1and2.bed"
},
"REPEATMASKER_DIR": "annotations/repeatMasker/",
"genomeToDHSpeaks": {
"hg38": "annotations/dhs/ENCFF301VRH.hg38.sorted.bed",
"mm10": "annotations/dhs/ENCFF108APF.bed"
},
"SIRVinfo": "annotations/SIRV_Set1_Lot00141_info-170612a.tsv"
}