Extractors #

UMIS and barcodes can be extracted from read names, sequences or tags.

To do so you define an extractor.

Available extractors are

Regular expression within read names #

Use a regular expression to extract from name

Example


[umi]
    # ...
    extract = { mode= 'RegexName', regex= 'umi=([ACTG]{8})' }

Extracts the first regex group. Follows rust regex syntax.

Search for a fixed string in in read names, then take the next N letters, optionally skipping some.

Example:

[umi]
    extract = {mode= 'SearchinName', search='umi|', length=8, skip=0}

(The extract sequence starts after search!).

Read from a BAM tag. Must be a string tag.

[umi]
    extract = {mode = 'Tag',  tag='XQ'}

Extract from a fixed region within the read

[umi]
    extract = {mode = 'ReadRegion',  start=4, stop=8}