Module: Umi whitelist - ComputationalSystemsBiology/Single-cell-RNA-seq GitHub Wiki

Identify correct cell barcodes, for umi-based protocols.

• Internal name : umiwhitelist

• Avalaible : local mode

• Input Ports :

  • fastq

• Output Ports :

  • whitelist_umi: text file with a list of correct cell barcodes (whitelist.txt)

• Optional parameters :

Parameter	Type	Description	Default Value
bc_pattern	string	Cellular barcode pattern - N = UMI position (required) ; C = cell barcode position (optional) ; X = sample position (optional)	CCCCCCCCCCCCCCCCNNNNNNNNNN
set_cell_number	integer	Explicity set the number of cell barcodes which should be accepted - Recommended value: 1000 - Default value 0 means no set cell number	0
expect_cells	integer	Upper limit estimate for the number of inputted cells - Recommended value: 1000 - Default value 0 means no expected cells number	0

More info: https://github.com/CGATOxford/UMI-tools/blob/master/doc/Single_cell_tutorial.md - look for "umi whitelist"