bam2fastq: Bam/Sam file to fastq file conversion

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Bam/Sam file to fastq file conversion

Description

Convert either paired or unpaired Bam file into fastq files.

Usage

  bam2fastq(bamFn, OUTPUT_PER_RG=TRUE, OUTPUT_DIR=".", paired=FALSE,
            fastqFns=sub("(\.bam|\.sam)$", "fastq", bamFn),
            fastq2Fns=sub("(\.bam|\.sam)$", "_R2.fastq", bamFn)
            )

Arguments

bamFn	character(1): path of input Bam/Sam files
OUTPUT_PER_RG	boolean(1): whether or not to output one fastq per RG. When TRUE, paired, fastqFns and fastq2Fns are ignoreed.
OUTPUT_DIR	boolean(1): the output dir for fastqs.
fastqFns	character(1): paths of first end of read file.
fastq2Fns	character(2): optional paths of second end of paired read file.
paired	boolean(1): paired-end or single-end read file.

Details

The conversion is done with picard's SamToFastq.

Rsamtools::testPairedEndBam cannot be used to test for paired or not. It doesn't work on Bam converted from fastq, due to the lack of header. paired has to be specified explicitly.

Value

invisible filenames of first read files.

Author(s)

Ge Tan

See Also

fastqs2bam

Examples

  ## Not run: 
    bamFn <- "/srv/gstore/projects/p2497/HiSeq4000_20171222_RUN420_o3705_fixedRG/20171222.A-SiCSeq_SCs_P5_unmapped.bam"
    bamFn <- "/scratch/gtan/p2497-SCCountQC/20171222.A-SiCSeq_SCs_P5_subset.bam"
    
    ## Split into one Fastq
    fastqFn <- bam2fastq(bamFn, fastqFns=sub("\\.bam$", ".fastq", basename(bamFn)), 
                         paired=FALSE)
    ## Split by RG
    fastqFn <- bam2fastq(bamFn, OUTPUT_PER_RG=TRUE, OUTPUT_DIR=".", paired=FALSE)
  
## End(Not run)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.