libV1.json

{
"linkers": [
    {"read": "read1", "start_min": 8, "start_max": 9, "name": "splint", "sequence":"TCAGAGC"}
],
"barcodes" : [
    {"read": "read1", "start": 0, "length": 9, "name": "lig", "sequences": "3lvlRNA_lig.txt", "level":2, "alias":"Ligation"},
    {"read": "read1", "anchor": "splint", "offset": 15, "length": 10, "name": "rt", "sequences": "guideRt.txt", "level":1, "alias":"RT"},
    {"read": "read1", "anchor": "splint", "offset": 7, "length": 8, "name": "umi", "type": "umi"},
    {"read": "index2", "start": 0, "length": 10, "name": "P7", "sequences": "3lvlRNA_pcr.txt", "level":3, "alias":"PCR"}
],
"sample_barcode": "rt",
"star_barcode_param": "--soloType CB_UMI_Simple --soloCBlen 29 --soloUMIstart 30 --soloUMIlen 8 --soloCBwhitelist None",
"bcl_convert": {
    "library_barcodes": {},
    "index2Seqs": "3lvlRNA_pcr.txt",
    "index2RevComp": false,
    "split_on": "index2"
}
}