fastqs2bam | R Documentation |
Convert multiple fastq files into Bam files and merged into one big Bam file with filenames as RG tag.
fastqs2bam(fastqFns, fastq2Fns=NULL, readGroupNames=NULL, bamFn,
platform="illumina", mc.cores=ezThreads())
fastqFns |
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fastq2Fns |
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readGroupNames |
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bamFn |
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platform |
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mc.cores |
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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.
invisible bamFn
.
Ge Tan
bam2fastq
## 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)
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