SCRenamer: Rename reads name in fastq

In wzthu/ATACFlow: An Easy-to-use Systematic pipeline for ATACseq data analysis

Rename reads name in fastq

Description

Rename reads name in fastq with increasing integer

Usage

atacSCRenamer(
  atacProc,
  fastqOutput1 = NULL,
  fastqOutput2 = NULL,
  fastqInput1 = NULL,
  fastqInput2 = NULL,
  interleave = FALSE,
  threads = getThreads(),
  ...
)

## S4 method for signature 'ATACProc'
atacSCRenamer(
  atacProc,
  fastqOutput1 = NULL,
  fastqOutput2 = NULL,
  fastqInput1 = NULL,
  fastqInput2 = NULL,
  interleave = FALSE,
  threads = getThreads(),
  ...
)

scRenamer(
  fastqInput1 = NULL,
  fastqInput2 = NULL,
  fastqOutput1 = NULL,
  fastqOutput2 = NULL,
  interleave = FALSE,
  threads = getThreads(),
  ...
)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacUnzipAndMerge unzipAndMerge
fastqOutput1	Character scalar. The output file path of renamed fastqInput1.
fastqOutput2	Character scalar. The output file path of renamed fastqInput2.
fastqInput1	Character scalar. For single-end sequencing, it contains sequence file paths. For paired-end sequencing, it can be file path with #1 mates paired with file path in file2 And it can also be interleaved file paths when argument interleave=TRUE
fastqInput2	Character scalar. It contains file path with #2 mates paired with file paths in fastqInput1 For single-end sequencing files and interleaved paired-end sequencing files(argument interleaved=TRUE), it must be NULL.
interleave	Character scalar. Set TRUE when files are interleaved paired-end sequencing data.
threads	Integer scalar. The threads will be created in this process. default: 1
...	Additional arguments, currently unused.

Details

The parameter related to input and output file path will be automatically obtained from ATACProc-class object(atacProc) or generated based on known parameters if their values are default(e.g. NULL). Otherwise, the generated values will be overwrited. If you want to use this function independently, you can use renamer instead.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

atacUnzipAndMerge unzipAndMerge atacQCReport atacRemoveAdapter

Examples

ignoreCheck() # warnning: run this for fast test only
library(magrittr)
td <- tempdir()
setTmpDir(td)

# Identify adapters
prefix<-system.file(package="esATAC", "extdata", "uzmg")
(reads_1 <-file.path(prefix,"m1",dir(file.path(prefix,"m1"))))
(reads_2 <-file.path(prefix,"m2",dir(file.path(prefix,"m2"))))

reads_merged_1 <- file.path(td,"reads1.fastq")
reads_merged_2 <- file.path(td,"reads2.fastq")
atacproc <-
atacUnzipAndMerge(fastqInput1 = reads_1,fastqInput2 = reads_2) %>%
atacRenamer

dir(td)

wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.