parse_10x_sam: Parse 10X bam file

In wenjie1991/CellBarocde: Cellular DNA Barcode Analysis toolkit

Parse 10X bam file

Description

Parse 10X bam file

Usage

parse_10x_sam(in_file_path, regex_str, cell_barcode_tag = "CR", umi_tag = "UR")

Arguments

in_file_path	A string, define the un-mapped sequences
regex_str	A string, define the regular expression to match the barcode sequence. The barcode sequence should be in the first catch. Please see the bc_extract for detail.
cell_barcode_tag	A string, define the tag of 10X cell barcode field in sam file. The default is "CR".
umi_tag	A string, define the tag of UMI field in the sam file.

Value

A data.frame with 4 columns:

1. cell_barcode: 10X cellular barcode.

2. umi: UMI sequence.

3. barcode_seq: lineage barcode.

4. count: reads count.

wenjie1991/CellBarocde documentation built on April 17, 2024, 4:41 a.m.