Rbowtie-package.RdThis package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool.
The package is used by the QuasR bioconductor package. We recommend to use
QuasR instead of using Rbowtie directly. QuasR provides a simpler
interface than Rbowtie and covers the whole analysis workflow of typical
high throughput sequencing experiments, starting from the raw sequence reads,
over pre-processing and alignment, up to quantification.
We also recommend to use Rhisat2 instead of SpliceMap for spliced alignment, which provides a more up-to-date and improved spliced short read aligner.
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10(3):R25 (2009).
Au KF, Jiang H, Lin L, Xing Y, Wong WH. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Research, 38(14):4570-8 (2010).