Parse 10X bam file

Parse 10X bam file

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.