r Biocpkg("Rbowtie") package provides an R wrapper around the popular
bowtie [@bowtie] short read aligner and around SpliceMap [@SpliceMap] a de novo
splice junction discovery and alignment tool, which makes use of the bowtie
The package is used by the
r Biocpkg("QuasR") [@QuasR] bioconductor package to
_qu_antify and _a_nnotate _s_hort _r_eads. We recommend to use the
package instead of using
r Biocpkg("Rbowtie") directly. The
package provides a simpler interface than
r Biocpkg("Rbowtie") and covers the
whole analysis workflow of typical ultra-high throughput sequencing experiments,
starting from the raw sequence reads, over pre-processing and alignment, up to
If you use
r Biocpkg("Rbowtie") [@Rbowtie] in your work, you can cite it as follows:
r Biocpkg("Rbowtie") is a package for the R computing environment and it is
assumed that you have already installed R. See the R project at
(http://www.r-project.org). To install the latest version of
you will need to be using the latest version of R.
r Biocpkg("Rbowtie") is
part of the Bioconductor project at (http://www.bioconductor.org). To get
r Biocpkg("Rbowtie") together with its dependencies you can use
if (!require("BiocManager")) install.packages("BiocManager") BiocManager::install("Rbowtie")
In order to run the code examples in this vignette, the
library need to be loaded.
Most questions about
r Biocpkg("Rbowtie") will hopefully be answered by the
documentation or references. If you've run into a question which isn't addressed
by the documentation, or you've found a conflict between the documentation and
software itself, then there is an active support community which can offer help.
The authors of the package (maintainer:
r maintainer("Rbowtie")) always appreciate
receiving reports of bugs in the package functions or in the documentation. The
same goes for well-considered suggestions for improvements.
Any other questions or problems concerning
r Biocpkg("Rbowtie") should be posted
to the Bioconductor support site (https://support.bioconductor.org). Users posting
to the support site for the first time should read the helpful posting guide at
(https://support.bioconductor.org/info/faq/). Note that each function in
has it's own help page, e.g.
help("bowtie"). Posting etiquette requires that you
read the relevant help page carefully before posting a problem to the site.
Please refer to the
r Biocpkg("Rbowtie") reference manual or the function documentation
?bowtie) for a complete description of
r Biocpkg("Rbowtie") functions.
The descriptions provided below are meant to give and overview over all functions
and summarize the purpose of each one.
To be able to align short reads to a genome, an index has to be build first using
bowtie_build. Information about arguments can be found with the help
bowtie_build_usage function or in the manual page
refFiles below is a vector with filenames of the reference sequence in
indexDir specifies an output directory for the index files that will
be generated when calling
refFiles <- dir(system.file(package="Rbowtie", "samples", "refs"), full=TRUE) indexDir <- file.path(tempdir(), "refsIndex") tmp <- bowtie_build(references=refFiles, outdir=indexDir, prefix="index", force=TRUE) head(tmp)
Information about the arguments supported by the
bowtie function can be obtained
with the help of the
bowtie_usage function or in the manual page
In the example below,
readsFiles is the name of a file containing short reads to
be aligned with
samFiles specifies the name of the output file with
the generated alignments.
readsFiles <- system.file(package="Rbowtie", "samples", "reads", "reads.fastq") samFiles <- file.path(tempdir(), "alignments.sam") bowtie(sequences=readsFiles, index=file.path(indexDir, "index"), outfile=samFiles, sam=TRUE, best=TRUE, force=TRUE) strtrim(readLines(samFiles), 65)
bowtie only generates ungapped alignments, the
SpliceMap function can be
used to generate spliced alignments.
SpliceMap is itself using
bowtie. To use
it, it is necessary to create an index of the reference sequence as described in
SpliceMap parameters are specified in the form of a named
list, which follows closely the configure file format of the original
program[@SpliceMap]. Be aware that
SpliceMap can only be used for reads that are
at least 50bp long.
readsFiles <- system.file(package="Rbowtie", "samples", "reads", "reads.fastq") refDir <- system.file(package="Rbowtie", "samples", "refs", "chr1.fa") indexDir <- file.path(tempdir(), "refsIndex") samFiles <- file.path(tempdir(), "splicedAlignments.sam") cfg <- list(genome_dir=refDir, reads_list1=readsFiles, read_format="FASTQ", quality_format="phred-33", outfile=samFiles, temp_path=tempdir(), max_intron=400000, min_intron=20000, max_multi_hit=10, seed_mismatch=1, read_mismatch=2, num_chromosome_together=2, bowtie_base_dir=file.path(indexDir, "index"), num_threads=4, try_hard="yes", selectSingleHit=TRUE) res <- SpliceMap(cfg) res strtrim(readLines(samFiles), 65)
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