SCReadCounts Read Grouping

The counts for aligned reads are tabulated by BAM file and, if desired, by a group identifier extracted from each alignment record. Use cases include cell-barcodes added for single-cell sequencing. Read groups 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 omitted from the output.

The available read-grouping strategies are defined in the file group.ini in the SCReadCounts distribution. New or modified read-grouping strategies can be created, using the same format, in a group.ini file in the current working directory. Named grouping strategies in the current working directory override those with the same name in the ReadCounts distribution.

Read-Grouping Strategies

UMI-tools

Pick out cell barcodes from read name/identifier added by umi_tools.

STARsolo

Cell barcodes added by STARsolo as CB tag in 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.

Read-Grouping 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]
Description: Pick out cell barcodes from read name/identifier added by umi_tools.
ReadNameWord: field_index=1 field_sep=_

STARsolo

[STARsolo]
Description: Cell barcodes added by STARsolo in CB tag in 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.
ReadTagValue: tag='CB' acceptlist='barcodes.tsv'

UMI-tools_Regex

[UMI-tools_Regex]
Description: Pick out cell barcodes from read name/identifier added by umi_tools using a regular expression.
ReadNameRegex: regex='_([ACGT]{16})_' regexgrp=1

UB-Tag

[UB-Tag]
Description: UB tag from aligned read, reads without a UB tag get value "XXXXXXXX"
ReadTagValue: tag='UB' missing='XXXXXXXX'