fastqs2bam: Fastq files to Bam with RG tag

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

Fastq files to Bam with RG tag

Description

Convert multiple fastq files into Bam files and merged into one big Bam file with filenames as RG tag.

Usage

  fastqs2bam(fastqFns, fastq2Fns=NULL, readGroupNames=NULL, bamFn,
             platform="illumina", mc.cores=ezThreads())

Arguments

fastqFns	character(n): paths of input fastq files
fastq2Fns	character(n): optional paths of the second read of paired-end data.
readGroupNames	character(n): read group IDs. Same length as fastqFns.
bamFn	character(1): filename of merged Bam file.
platform	character(1): the platform used.
mc.cores	integer(1): the threads to run.

Details

Each fastq file first is converted into Bam file with filename as “LB” and readGroupNames as ‘ID’ and ‘SM’ in RG tag using picard's FastqToSam. Then Bam files are merged into one big Bam file using picard's MergeSamFiles with a sort order by queryname.

Value

invisible bamFn.

Author(s)

Ge Tan

See Also

bam2fastq

Examples

  ## Not run: 
    fastqFns <- list.files(path="/srv/gstore/projects/p2288/HiSeq2500_20171011_RR99_o3511/dmx",
                           pattern="\\.fastq\\.gz$", full.names=TRUE)
    fastqFns <- fastqFns[1:5]
    fastqs2bam(fastqFns,
               readGroupNames=sub("\\.(fastq|fq)(\\.gz){0,1}$", "", 
                                  basename(fastqFns)),
               bamFn="20171011.A-C1_HT_24H_unmapped.bam")
    
    ## Make uBAM from cell dataset.tsv
    input <- EzDataset(file="/srv/gstore/projects/p2488/HiSeq4000_20180209_RUN424_o3954/scFastq_dataset.tsv", 
                       dataRoot="/srv/gstore/projects")
    fastqs2bam(fastqFns=input$getFullPaths("Read1"),
               readGroupNames=input$getNames(),
               bamFn="20180209.B-single_cell_hippo_neurons_E1_1_unmapped.bam",
               mc.cores = 4)
  
## End(Not run)

uzh/ezRun documentation built on May 9, 2024, 6:16 p.m.