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example_config.json
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example_config.json
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{
"Primer3" : {
"PRIMER_TASK" : "pick_detection_primers",
"PRIMER_PICK_LEFT_PRIMER" : 1,
"PRIMER_PICK_RIGHT_PRIMER" : 1,
"PRIMER_NUM_RETURN" : 3,
"PRIMER_PRODUCT_SIZE_RANGE" : "80-150",
"PRIMER_MIN_SIZE" : 18,
"PRIMER_OPT_SIZE" : 22,
"PRIMER_MAX_SIZE" : 27,
"PRIMER_MIN_GC" : 40,
"PRIMER_MAX_GC" : 80,
"PRIMER_OPT_GC_PERCENT" : 60,
"PRIMER_MIN_TM" : 58,
"PRIMER_OPT_TM" : 60,
"PRIMER_MAX_TM" : 62,
"PRIMER_PAIR_MAX_DIFF_TM" : 1,
"PRIMER_TM_FORMULA" : 1,
"PRIMER_SALT_CORRECTIONS" : 1,
"PRIMER_SALT_MONOVALENT" : 50,
"PRIMER_SALT_DIVALENT" : 0,
"PRIMER_MAX_TEMPLATE_MISPRIMING" : 10,
"PRIMER_MAX_NS_ACCEPTED" : 0,
"PRIMER_MAX_POLY_X" : 5,
"PRIMER_TM_FORMULA" : 0,
"PRIMER_SALT_CORRECTIONS" : 0
},
"Bio::SeqFetcher::Ensembl::TranscriptIDtocDNASeq" : {
"species" : "mouse"
},
"Bio::SeqFetcher::Ensembl::TranscriptIDtocDNASeq::WithExons" : {
"species" : "mouse"
},
"Bio::SeqFetcher::Ensembl::GeneIDtoGenomicSeq" : {
"species" : "mouse"
},
"Bio::SeqFetcher::Ensembl::ChromosomePositiontoGenomicSeq" : {
"species" : "mouse"
},
"Bio::SeqFetcher::Ensembl::GeneIDtoGenomicSeq::Promoter" : {
"species" : "mouse",
"upstream" : 300,
"downstream" : 100
},
"Buckley::PrimerDesigner::PreProcess::RepeatMask" : {
"species" : "mouse",
"nolow" : "1",
"verbose" : "1",
"path" : "/usr/local/RepeatMasker"
},
"Buckley::PrimerDesigner::PostProcess::UnafoldMelt" : {
"max_tm" : 65,
"program_name" : "melt.pl",
"NA" : "DNA",
"sodium" : 0.05,
"temperature" : 60,
"magnesium" : 0.003
}
}