Alignment of DNA-seq reads

Alignment of DNA-seq reads

align_dna(threads = 1, output.dir = ".", hisat2 = "hisat2",
  samtools = "samtools", sambamba = "sambamba", species = c("human",
  "mouse"), idx = NULL, reads1 = NULL, reads2 = NULL, fastq = TRUE,
  fasta = FALSE, softClipPenalty = NULL, noSoftClip = FALSE,
  tmo = FALSE, secondary = FALSE, maxAlign = NULL, nomixed = FALSE,
  nodiscordant = FALSE, rgid = NULL, quiet = FALSE,
  non_deterministic = FALSE, maxInsert = NULL, memory = "1G",
  remove.mitochondrial = "MT", remove.duplicates = TRUE,
  hash_table = 262144, overflow_size = 2e+05, io_buffer = 128)

Arguments

threads	an integer value indicating the number of parallel threads to be used by FastQC. [DEFAULT = maximum number of available threads - 1].
output.dir	character string specifying the directory to which results will be saved. If the directory does not exist, it will be created.
hisat2	a character string specifying the path to the hisat2 executable. [DEFAULT = "hisat2"].
samtools	a character string specifying the path to the samtools executable. [DEFAULT = "samtools"].
sambamba	a character string specifying the path to the sambamba executable. [DEFAULT = "sambamba"].
species	character string specifying the name of the species. Only 'human', and 'mouse' are supported at present. [DEFAULT = human].
idx	character vector specifying 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. If NULL then the index for the relevant species (human or mouse) will be created using the build_index() function.
reads1	Character vector of mate1 reads. If specified, then reads.dir must be NULL.
reads2	Character vector of mate2 reads. If specified, then reads.dir must be NULL. Must be the same length as mate1. If single-end sequencing, then should be left as NULL.
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.
tmo	Logical indicating whether to report only those reads aligning to known transcripts.
secondary	Logical indicating whether to report secondary alignments.
maxAlign	Integer indicating the maximum number of distinct primary alignments to search for each read.
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.
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.
maxInsert	The maximum fragment length for valid paired-end alignments. This option is valid only with noSplice = TRUE.
memory	String specifying maximum memory per thread; suffix K/M/G recognized.
remove.mitochondrial	Character string. If set, this will remove reads mapping to the mitochondrial genome. The string should match the reference name for the mitochindrial genome in the alignment file. Examples include "ChrM", "M" and "MT".
remove.duplicates	If TRUE, duplicate reads will be removed.
hash_table	Size of hash table for finding read pairs (default is 262144 reads); will be rounded down to the nearest power of two. For best performance should be > (average coverage) * (insert size).
overflow_size	Size of the overflow list where reads, thrown out of the hash table, get a second chance to meet their pairs (default is 200000 reads); increasing the size reduces the number of temporary files created.
io_buffer	Controls sizes of the two buffers (in MB) used for reading and writing BAM during the second pass (default is 128).

Value

Raw and filtered BAM files