SCExecute Cell Barcodes

SCExecute splits the aligned reads by cell barcodes extracted from each alignment record. Cell barcodes can be extracted from read headers by regular expression, splitting lines according to some separator character, or directly from BAM alignment headers. Aligned reads without a group identifier can be assigned a specific identifier or skipped.

The available cell-barcode strategies are defined in the file group.ini in the SCExecute distribution. New or modified cell-barcode strategies can be created, using the same format, using a similar group.ini file in the current working directory. Named cell-barcode extraction rules in the current working directory override those with the same name in the SCExecute distribution.

Cell Barcode Extraction Rules

UMI-tools

Cell barcodes from read name added by UMI-tools.

STARsolo

Cell barcodes from the CB tag of aligned read - reads without a CB tag or with CB tag not in the accept list (default: file “barcodes.tsv” in the current directory) dropped

CellRanger

Cell barcodes from the CB tag of aligned read - reads without a CB tag or with CB tag not in the accept list (default: file “barcodes.tsv” in the current directory) dropped

Cell Barcode Extraction Operations

ReadNameWord

Parameters: field_index field_sep=_ missing=None

Split the read name into words according to field_sep (default: “_”), and retain word with index field_index (required). Field index starts at 0. If the read name does not have enough words, use the read group identifier specified by missing (default: not specified). If missing is not specified, drop the read.

ReadNameRegex

Parameters: regex regexgrp=1 missing=None

Apply (Python) regular expression regex (required) to the read name and extract matching group number regexgrp (default: 1). If the regular expression doesn’t match, use the read group identifier specified by missing (default: not specified). If missing is not specified, drop the read.

ReadTagValue

Parameters: tag missing=None

Use the value in the BAM tag tag (required). If tag is missing, use the read group specified by identifier missing (default: not specified). If missing is not specified, drop the read.

RGTag

Parameters: missing=None

Use the value in the BAM read-group tag “RG”. If “RG” is missing, use the read group specified by identifier missing (default: not specified). If missing is not specified, drop the read.

Examples

UMI-tools

[UMI-tools_CB]
Name: UMI-tools
Description: Cell barcodes from read name added by umi_tools.
Type: CellBarcode
ReadNameWord: field_index=1 field_sep=_

STARsolo

[STARsolo_CB]
Name: STARsolo
Description: Cell barcodes from the CB tag of aligned read - reads without a CB tag or with CB tag not in the accept list (default: file "barcodes.tsv" in the current directory) dropped.                                                                
Type: CellBarcode                                                                                                            
ReadTagValue: tag='CB' acceptlist='barcodes.tsv'

UMI-tools_Regex

[UMI-tools_Regex_CB]
Name: UMI-tools-RE
Description: Pick out cell barcodes from read name/identifier added by umi_tools using a regular expression.
Type: CellBarcode
ReadNameRegex: regex='_([ACGT]{16})_' regexgrp=1 missing="XXXXXXXXX"

See Also

SCExecute Home, Usage, Input Files, Command/Template Substitution, Examples