bam.process: Bam File Process Function

In morris-lab/CloneHunter: Identify Clonal Identity from ScRNA-Seq and CellTag Data

Description

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

Usage

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

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

morris-lab/CloneHunter documentation built on June 12, 2019, 11:01 a.m.