hisat2R: hisat2R
In msubirana/ergWgsTools: What the Package Does (One Line, Title Case)

Parser of HISAT2 for R

1	hisat2R(threads, type, index, fastq_file, out_path)

`type`	"single" or "paired" format
`index`	HISAT2 reference genome index
`fastq_file`	Fastq to demultiplex. In paired-end file used should be R1 and following the format "file_R1.*"
`out_path`	Path where to save the demultiplex output

threads <- 2
index <- '/imppc/labs/lplab/share/marc/refgen/hg38/HISAT2/hg38.tar.gz'
fastq_file <- '/imppc/labs/lplab/share/Insulinoma/raw/NET20_INS_RNA_1.fq.gz'
out_path <- '/imppc/labs/lplab/share/Insulinoma/raw/proves'
type <- 'paired'

hisat2R(threads, type, index, fastq_file, out_path)