bam.process: Bam File Process Function

Description Usage Arguments Value Examples

View source: R/CellTagExtraction_Function.R

Description

This function extracts CellTags from the bam sequencing file, provides cell barcode, umi and their corresponding celltag information.

Usage

1
bam.process(bam.file, pattern, short.nt.before.tag, short.nt.after.tag)

Arguments

bam.file

The input bam data directory

pattern

The pattern to seek for

short.nt.before.tag

A short sequence before the 8nt tag to help more specific identification

short.nt.after.tag

A short sequence after the 8nt tag to help more specific identification

Value

A data table contains cell barcode, celltag and umi information

Examples

1
bam.process("data.fastq", "CCGGT[ATCG]{8}GAATTC", "CCGGT", "GAATTC")

morris-lab/CloneHunter documentation built on Jan. 6, 2019, 3:04 a.m.