extractBcAndUb: Extract barcode and UMI in reads with umi_tools

In BMILAB/scAPAtrap: Identification and Quantification of Alternative Polyadenylation Sites from Single-cell RNA-seq Data

Extract barcode and UMI in reads with umi_tools

Description

Extract barcode and UMI in reads with umi_tools

Usage

extractBcAndUb(umitools.path, pattern, input.seq, whitelist, ...)

Arguments

umitools.path	The path of the umi_tools.
pattern	The pattern used to represent barcode and UMI (e.g If the barcode length is 8 and the UMI length is 4, then the pattern=CCCCCCCCNNNN)
input.seq	Path of the fastq file, which must contain two paths with the first one recording barcode and UMI information.
whitelist	whitelist barcode.
...	Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If 'TRUE' basic status updates will be printed along the way. logf If not NULL, then it should be a character string denoting a file name. Then message will be written to 'logf'. notRun Default is FALSE. If 'TRUE', the Shell commands inside this function will not run but output the commad line.

Value

The path of Read2 (<input.seq[2]>.extracted.fastq)

Examples

umitools.path <-  '/home/dell/miniconda3/envs/scAPA/bin/umi_tools'
input.seq <- c('./fastq/SRR1610598_1.fastq','./fastq/SRR1610598_2.fastq')
pattern <- 'CCCCCCCCNNNN'
whitelist <- './fastq/whitelist.txt'
## Not run: 
extractBcAndUb(umitools.path, pattern, input.seq, whitelist)

## End(Not run)
extractBcAndUb(umitools.path, pattern, input.seq, whitelist, notRun=TRUE)

BMILAB/scAPAtrap documentation built on Oct. 13, 2023, 2:36 a.m.