Commit c0e49915 authored by Audrey BIHOUEE's avatar Audrey BIHOUEE
Browse files

From 3 to 2 config files; updated snakefile with one more fastqc and multiQC on STAR

parent 006e01ca
{
"outdir":"Results/",
"reference":"Ensembl_GRCh37",
"reference":
{
"name":"Ensembl_GRCh37",
"description":"Homo sapiens Ensembl GRCh37",
"STARindexDir":"index-star-75b",
"fasta":"/commun/data/pubdb/ensembl/Hs/b37/human_g1k_v37.fasta",
"gtf":"/commun/data/pubdb/ensembl/Hs/b37/Homo_sapiens.GRCh37.75_short.gtf",
"biomart":"feb2014.archive.ensembl.org,ENSEMBL_MART_ENSEMBL,hsapiens_gene_ensembl"
},
"replicates":{
"CT": {
"name":"CT",
"samples":["80_CT_1_chr22","81_CT_2_chr22","82_CT_3_chr22","83_CT_4_chr22"]
"J0_CTRL": {
"name":"J0_CTRL",
"samples":["1_J0-1-ctrl","6_J0-2-ctrl","11_J0-3-ctrl"]
},
"BEZ": {
"name":"BEZ",
"samples":["96_BEZ_1_chr22","97_BEZ_2_chr22","98_BEZ_3_chr22","99_BEZ_4_chr22"]
"J3_CTRL": {
"name":"J3_CTRL",
"samples":["2_J3-1-ctrl","7_J3-2-ctrl","12_J3-3-ctrl"]
},
"J6_CTRL": {
"name":"J6_CTRL",
"samples":["4_J6-1-ctrl","9_J6-2-ctrl","14_J6-3-ctrl"]
},
"J3_LSD1": {
"name":"J3_LSD1",
"samples":["3_J3-1-LSD1","8_J3-2-LSD1","13_J3-3-LSD1"]
},
"J6_LSD1": {
"name":"J6_LSD1",
"samples":["5_J6-1-LSD1","10_J6-2-LSD1","15_J6-3-LSD1"]
}
},
},
"prinseq-meanquality":"30",
"cutadapt-forward":"AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
"cutadapt-reverse":"AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
"library-type":"fr-secondstrand",
"read-length":"100",
"align-cpu":"10",
"genomeDir":"CONFIG/genome"
"library-type":"reverse",
"read-length":"75",
"align-cpu":"10"
}
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