run_hisat2: Run HISAT2

In GrahamHamilton/pipelineTools: Pipeline Tools for NGS Sequence Analysis Pipelines

Run HISAT2

Description

Runs the HISAT2 tool, can be used for single end and paired end reads

Usage

run_hisat2(
  input1 = NULL,
  input2 = NULL,
  index = NULL,
  sample.name = NULL,
  strandedness = NULL,
  no_splice = FALSE,
  known_splice = NULL,
  assembly = FALSE,
  phred = 33,
  threads = 10,
  out.dir = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  hisat2 = NULL,
  version = FALSE
)

Arguments

input1	List of the paths to files containing to the forward reads, required
input2	List of the paths to files containing to the reverse reads, required for paired end sequence data
index	Path to the reference genome hisat2 index, required
sample.name	List of the sample names, required
strandedness	Strand-specific information
no_splice	Disable spliced alignment, use for Trypanosomes
known_splice	File with known splice sites
assembly	Reports alignments tailored for transcript assemblers
phred	Quality score offsets, default set to illumina/sanger standard of 33
threads	Number of threads for hisat2 to use, default set to 10
out.dir	Name of the directory from the HISAT2 output. If NULL, which is the default, a directory named "hisat2_alignments" is created in the current working directory.
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
execute	Whether to execute the commands or not, default set to TRUE
hisat2	Path to the HISAT2 program, required
version	Returns the version number

Value

A list with the HISAT2 commands

Examples

## Not run: 
 trimmed_reads_dir <- "trimmed_reads"
 mate1 <- list.files(path = trimmed_reads_dir, pattern = "*_R1_001.fastq$", full.names = TRUE)
 mate2 <- list.files(path = trimmed_reads_dir, pattern = "*_R2_001.fastq$", full.names = TRUE)

 sample_names <- unlist(lapply(strsplit(list.files(path = trimmed_reads_dir,
                        pattern = "*_R1_001.fastq$",
                        full.names = FALSE),"_"), `[[`, 1))

 index <- "/export/buzz1/Genome/Homo_sapiens/Ensembl/GRCH38_p7/Sequence/Transcriptome/
           KallistoIndex/GRCh38_p7.kall"

 # Paired End example
 strandedness <- "RF"
 hisat2.cmds <- run_hisat2(input1 = mate1,
                           input2 = mate2,
                           index = genome,
                           sample.name = sample.names,
                           strandedness = strandedness,
                           assembly = TRUE,
                           out.dir = hisat.alignments.dir,
                           hisat2 = "/software/hisat_v2-2.1.0/hisat2")

 # Single End example
 strandedness <- "R"
 hisat2.cmds <- run_hisat2(input1 = mate1,
                           index = genome,
                           sample.name = sample.names,
                           strandedness = strandedness,
                           assembly = TRUE,
                           out.dir = hisat.alignments.dir,
                           hisat2 = "/software/hisat_v2-2.1.0/hisat2")
 
## End(Not run)

GrahamHamilton/pipelineTools documentation built on Dec. 8, 2024, 3:53 p.m.