run_hisat2: Wrapper script to run HISAT2.
In anilchalisey/chompR: ChIP and ATAC-seq data processing pipeline

Description Usage Arguments Value Examples

Script to align reads to a reference genome using hisat2. This requires an existing index which may be created using hisat2 itself. Commonly used genome indices may also be downloaded from the HISAT2 homepage.

run_hisat2(hisat2 = "hisat2", idx = NULL, mate1 = NULL,
  mate2 = NULL, fastq = TRUE, fasta = FALSE,
  softClipPenalty = NULL, noSoftClip = FALSE, noSplice = FALSE,
  knownSplice = NULL, strand = NULL, tmo = FALSE, maxAlign = NULL,
  secondary = FALSE, minInsert = NULL, maxInsert = NULL,
  nomixed = FALSE, nodiscordant = FALSE, threads = 1, rgid = NULL,
  quiet = FALSE, non_deterministic = FALSE)

`hisat2`	Path to hisat2 (if using WSL, then this should be the full path on the linux subsystem)
`idx`	The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final .1.ht2, etc.
`mate1`	Comma-separated list of files containing mate 1s (filename usually includes _1)
`mate2`	Comma-separated list of files containing mate 2s (filename usually includes _2). Sequences specified with this option must correspond file-for-file and read-for-read with those specified in .
`fastq`	Logical indicating if reads are FASTQ files.
`fasta`	Logical indicating if reads are FASTA files.
`softClipPenalty`	Sets the maximum (MX) and minimum (MN) penalties for soft-clipping per base, both integers. Must be given in the format "MX,MN".
`noSoftClip`	Logical indicating whether to disallow soft-clipping.
`noSplice`	Logical indicating whether to switch off spliced alignment, e.g., for DNA-seq analysis.
`knownSplice`	Path to text file containing known splice sites.
`strand`	Specify strand-specific information. Default is unstranded.
`tmo`	Logical indicating whether to report only those reads aligning to known transcripts.
`maxAlign`	Integer indicating the maximum number of distinct primary alignments to search for each read.
`secondary`	Logical indicating whether to report secondary alignments.
`minInsert`	The minimum fragment length for valid paired-end alignments. This option is valid only with noSplice = TRUE.
`maxInsert`	The maximum fragment length for valid paired-end alignments. This option is valid only with noSplice = TRUE.
`nomixed`	By default, when hisat2 cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. If TRUE, this option disables that behavior.
`nodiscordant`	By default, hisat2 looks for discordant alignments if it cannot find any concordant alignments. If true, this option disables that behavior.
`threads`	an integer value indicating the number of workers to be used. If NULL then one less than the maximum number of cores will be used. [DEFAULT = NULL].
`rgid`	Character string, to which the read group ID is set.
`quiet`	If TRUE, print nothing except alignments and serious errors.
`non_deterministic`	When set to TRUE, HISAT2 re-initializes its pseudo-random generator for each read using the current time.

Alignment file in SAM format

## Not run: 
run_hisat2(hisat2 = "hisat2", idx = "../prana/data-raw/index/UCSC.hg19",
mate1 = "../prana/data-raw/seqFiles/HB1_sample_1.fastq.gz",
mate2 = "../prana/data-raw/seqFiles/HB1_sample_2.fastq.gz",
fastq = TRUE, fasta = FALSE, softClipPenalty = NULL, noSoftClip = FALSE,
noSplice = FALSE, knownSplice = NULL, strand = NULL, tmo = FALSE,
maxAlign = NULL, secondary = FALSE, minInsert = NULL, maxInsert = NULL,
nomixed = FALSE, nodiscordant = FALSE,
threads = (parallel::detectCores() - 1), rgid = NULL, quiet = FALSE,
non_deterministic = TRUE)

## End(Not run)