fastq.process: Fastq Process Function

Description Usage Arguments Value Examples

View source: R/CellTagExtraction_Function.R

Description

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

Usage

1
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

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

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