Module: Umi extract

Extract UMI barcode from a read and add it to the read name, leaving any sample barcode in place. Can deal with paired-end reads and UMIs split across the two ends. Can also optionally extract cell barcodes and append these to the read name.

• Internal name : umiextract

• Avalaible : local mode

• Input Ports :

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

• Output Ports :

  • fastq

• 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
qft	integer	(quality filter threshold) Remove reads where any UMI base quality score falls below this threshold	30
encoding	string	Base score encoding	phred33

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