Updating JSON #2
Description
{
"project": {
"name": "My DGE Analysis",
"interaction": true,
"lfc_cutoff": 2,
"p_cutoff": 0.05,
"data_source": "ncbi",
"organism": {
"name":"Homo Sapiens",
"species_code": "Hs",
"gtf": "",
"reference": ""},
"output_dir": "/home/genwork2/Mert/RNAseq/EDGEROUTPUTS",
"factors": [
{
"name": "treatment",
"levels": ["HBR","UHR"]
},
{
"name": "drug",
"levels": ["A","B"]
}
],
"samples": [
{
"id":1,
"sample_name":"HBR_Rep1",
"countFile": "/home/genwork2/Mert/RNAseq/ALIGNEROUTPUTFE/read_counts/HBR_Rep1/gene_level_counts.txt",
"factors": {
"treatment": "HBR",
"drug": "A"
}
},
{ "sample_id":2,
"sample_name": "HBR_Rep2",
"countFile": "/home/genwork2/Mert/RNAseq/ALIGNEROUTPUTFE/read_counts/HBR_Rep2/gene_level_counts.txt",
"factors": {
"treatment": "HBR",
"drug": "A"
}
},
{ "sample_id": 3,
"sample_name": "HBR_Rep3",
"countFile": "/home/genwork2/Mert/RNAseq/ALIGNEROUTPUTFE/read_counts/HBR_Rep3/gene_level_counts.txt",
"factors": {
"treatment": "HBR",
"drug": "B"
}
},
{
"sample_id": 4,
"sample_name": "UHR_Rep1",
"countFile": "/home/genwork2/Mert/RNAseq/ALIGNEROUTPUTFE/read_counts/UHR_Rep1/gene_level_counts.txt",
"factors": {
"treatment": "UHR",
"drug": "A"
}
},
{
"sample_id": 5,
"sample_name": "UHR_Rep2",
"countFile": "/home/genwork2/Mert/RNAseq/ALIGNEROUTPUTFE/read_counts/UHR_Rep2/gene_level_counts.txt",
"factors": {
"treatment": "UHR",
"drug": "A"
}
},
{
"sample_id": 6,
"sample_name": "UHR_Rep3",
"countFile": "/home/genwork2/Mert/RNAseq/ALIGNEROUTPUTFE/read_counts/UHR_Rep3/gene_level_counts.txt",
"factors": {
"treatment": "UHR",
"drug": "B"
}
}
],
"contrasts": [ >> this one should be created >> for all contrasts and their interactions... >>> store filepaths here.
{
"name": "HBR_vs_UHR",
"factor": "treatment",
"levelA": "HBR",
"levelB": "UHR"
},
{
"name": "drugA_vs_B",
"factor": "drug",
"levelA": "A",
"levelB": "B"
}
]
}
}