tests/Bowtie2Alignment,PE.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

library("aroma.seq")

fullTest <- (Sys.getenv("_R_CHECK_FULL_") != "")
fullTest <- fullTest && isCapableOf(aroma.seq, "bowtie2")
if (fullTest) {

# Setup (writable) local data directory structure
setupExampleData()

dataSet <- "TopHat-example"
organism <- "Lambda_phage"

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# Setup FASTA reference file
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fa <- FastaReferenceFile$byOrganism(organism)
print(fa)


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# Setup FASTQ set
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fqs <- FastqDataSet$byName(dataSet, organism=organism, paired=TRUE)
print(fqs)


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# Build index set
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is <- buildBowtie2IndexSet(fa, verbose=-10)
print(is)


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# Paired-end alignment
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alg <- Bowtie2Alignment(fqs, indexSet=is)
print(alg)

bams <- process(alg, verbose=-20)
print(bams)

# Display an example BAM file
for (ii in seq_along(bams)) print(bams[[ii]])

} # if (fullTest)


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# HISTORY:
# 2013-08-24
# o Created from non-paired version.
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