fastq.process: Fastq Process Function

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

Description

This function extracts CellTags from the raw fastq sequencing file, provides counts of each CellTag and sorts them in desending order.

Usage

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

Arguments

fastq.file	The input fastq/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 list contains count table of CellTags. If requested to save fullTag counts, i.e. save.fullTag.counts = TRUE, return a list of both 8nt tags and full sequences count. Otherwise, a list of 8nt tags counts.

Examples

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

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