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 paired ends. Can also optionally extract cell barcodes and append these to the read name also.

• Internal name : umi_extract

• Avalaible : local mode

• Input Ports :

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

• Output Ports :

  • fastq

• Optional parameters :

  • bc_pattern : Cellular barcode pattern (identifies bases position) - N = UMI position (required) ; C = cell barcode position (optional) ; X = sample position (optional)
  • quality_filter_threshold: Remove reads where any UMI base quality score falls below this threshold - Usage : quality-filter-threshold=30
  • quality_filter_mask: If a UMI base has a quality below this threshold, replace the base with 'N' - Usage : quality-filter-mask=10

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