GSTRUCT suite

Description Usage Arguments Value Author(s)

Given a set of alignments, align them to a genome using the GSNAP algorithm. The GSNAP algorithm contains a number of features making it a very high quality algorithm for dealing with short reads and those from RNA-seq data in particular. Via the GsnapParam class and the gsnap function, R users are given complete control over GSNAP.

## S4 method for signature 'character,character_OR_NULL,GsnapParam'
gsnap(input_a, input_b, params,
                   output = file.path(getwd(),
                                      file_path_sans_ext(basename(input_a),
                                                         TRUE)),
                   consolidate = TRUE, ...)

`input_a`	A path to the FASTA file containing reads to align against a `GmapGenome` object. If the sequencing data is single-end, this is the only FASTA file used as input.
`input_b`	If provided, a path to the FASTA file containing the second set of reads from paired-end sequencing data.
`params`	A `GsnapParam` object to configure the behavior of GSNAP.
`output`	The output path for the GSNAP alignments. The results will be saved in `dirname(output)`. If `split_output` in `params` is `TRUE`, `basename(output)` is used as the common stem for the multiple output files. Otherwise, the results are saved to a single SAM file, its path formed by adding the “sam” extention to `output`.
`consolidate`	If GSNAP is run with multiple worker threads, each thread will output its own set of files. If consolidate is set to TRUE, these files will be merged. The default is TRUE.
`...`	Additional arguments to pass to GSNAP not specifically supported by the `gmapR` package.