config_cls3.json

{
	"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": "CLS3",
	"PROJECT_LONG_NAME": "GENCODE CLS Phase 3",
	"PROJECT_CONTACT_EMAIL": "julien.lagarde@crg.eu",
	"TRACK_HUB_BASE_URL": "https://public-docs.crg.es/rguigo/Data/jlagarde/gencode/trackHubs/CLS3/",
	"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"
}