trimbatch: Genome read coverage by transcript models

In tgirke/systemPipeR: systemPipeR: Workflow Environment for Data Analysis and Report Generation

Genome read coverage by transcript models

Description

## Trims adaptors hierarchically from longest to shortest match from right end of read. ## If 'internalmatch=TRUE' then internal matches will trigger the same behavior. The ## argument minpatternlength defines shortest adaptor match to consider for reads ## containing only partial adaptors at the right end.

Usage

trimbatch(fq, pattern, internalmatch=FALSE, minpatternlength=8, 
                            Nnumber=1, polyhomo=100, minreadlength=18, 
                            maxreadlength)

Arguments

fq	character path to fastq file that contains the target sequences.
pattern	character pattern used to trim the sequence.
internalmatch	The default is FALSE. Trims adaptors hierarchically from longest to shortest match from right end of read. If 'internalmatch=TRUE' then internal matches will trigger the same behavior.
minpatternlength	It defines shortest adaptor match to consider for reads containing only partial adaptors at the right end.
Nnumber	A numeric value representing a minimum criterion for the filter. It selects elements with fewer than Nnumber 'N' symbols in each element.
polyhomo	A numeric value representing a maximum criterion for the filter. It selects elements with fewer than threshold copies of any nucleotide.
minreadlength	numeric value representing minimum read length.
maxreadlength	numeric value representing maximun read length.

Author(s)

Thomas Girke

Examples

## Preprocessing of paired-end reads
dir_path <- system.file("extdata/cwl/preprocessReads/trim-pe", package="systemPipeR")
targetspath <- system.file("extdata", "targetsPE.txt", package="systemPipeR")
trim <- loadWorkflow(targets=targetspath, wf_file="trim-pe.cwl", input_file="trim-pe.yml", dir_path=dir_path)
trim <- renderWF(trim, inputvars=c(FileName1="_FASTQ_PATH1_", FileName2="_FASTQ_PATH2_", SampleName="_SampleName_"))
trim
## Not run: 
iterTrim <- "trimbatch(fq, pattern='ACACGTCT', internalmatch=FALSE, minpatternlength=6, Nnumber=1, polyhomo=50, minreadlength=16, maxreadlength=101)" 
preprocessReads(args=trim[1], Fct=iterTrim, batchsize=100000, overwrite=TRUE, compress=TRUE)

## End(Not run)

tgirke/systemPipeR documentation built on Sept. 24, 2024, 9:48 a.m.