def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'celseq2'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=6,
barcodeRead=0,
barcodeStart=6,
barcodeLength=8,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'CS2C8U6'
self.longName = 'CELSeq 2, CB: 8bp, UMI: 6bp'
self.autoDetectable = True
self.description = 'R1 starts with a 6bp UMI followed by a 8bp cell barcode'
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'celseq2_noNla'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=8,
barcodeRead=0,
barcodeStart=8,
barcodeLength=8,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'CS2C8U8NNLA'
self.longName = 'CELSeq 2, CB: 8bp, UMI: 8bp, NLAIII free'
self.autoDetectable = True
self.description = 'CEL-Seq2 without NLAIII digestable barcodes '
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'scartrace'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=0,
barcodeRead=0,
barcodeStart=0,
barcodeLength=8,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'SCARC8R1'
self.longName = 'Scartrace, CB: 8bp'
self.description = '384 well format. Scar amplicon demultiplexing, cell barcode in read 1'
self.autoDetectable = True
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'lennart96NLA'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=3,
barcodeRead=0,
barcodeStart=3,
barcodeLength=8,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'NLAIII96C8U3'
self.longName = 'NLAIII, 96well CB: 8bp UMI: 3bp'
self.autoDetectable = True
self.description = '96 well format. 3bp umi followed by 8bp barcode'
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'maya_mspj1'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=3,
barcodeRead=0,
barcodeStart=3,
barcodeLength=8,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'MSPJIC8U3'
self.longName = 'MSPJI, CB: 8bp UMI: 3bp'
self.autoDetectable = True
self.description = 'MSPJI barcoded fragments. 3bp umi followed by 8bp cell barcode.'