Minimap2 Align to Genome

Uses minimap2 to align sequences agains a reference databse. Uses options '-ax splice -t 12 -k14 –secondary=no fa_file fq_in'

Usage

minimap2_align(
  config,
  fa_file,
  fq_in,
  annot,
  outdir,
  minimap2 = NA,
  k8 = NA,
  samtools = NA,
  prefix = NULL,
  threads = 1
)

Arguments

config

Parsed list of FLAMES config file

fa_file

Path to the fasta file used as a reference database for alignment

fq_in

File path to the fastq file used as a query sequence file

annot

Genome annotation file used to create junction bed files

outdir

Output folder

minimap2

Path to minimap2 binary

k8

Path to the k8 Javascript shell binary

samtools

path to the samtools binary, required for large datasets since Rsamtools does not support CSI indexing

prefix

String, the prefix (e.g. sample name) for the outputted BAM file

threads

Integer, threads for minimap2 to use, see minimap2 documentation for details, FLAMES will try to detect cores if this parameter is not provided.

Value

a data.frame summarising the reads aligned

See also

[minimap2_realign()]

Examples

temp_path <- tempfile()
bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE)
file_url <- 'https://raw.githubusercontent.com/OliverVoogd/FLAMESData/master/data'
fastq1 <- bfc[[names(BiocFileCache::bfcadd(bfc, 'Fastq1', paste(file_url, 'fastq/sample1.fastq.gz', sep = '/')))]]
genome_fa <- bfc[[names(BiocFileCache::bfcadd(bfc, 'genome.fa', paste(file_url, 'SIRV_isoforms_multi-fasta_170612a.fasta', sep = '/')))]]
annotation <- bfc[[names(BiocFileCache::bfcadd(bfc, 'annot.gtf', paste(file_url, 'SIRV_isoforms_multi-fasta-annotation_C_170612a.gtf', sep = '/')))]]
outdir <- tempfile()
dir.create(outdir)
if (!any(is.na(sys_which(c("minimap2", "k8"))))) {
    minimap2_align(
        config = jsonlite::fromJSON(system.file('extdata/SIRV_config_default.json', package = 'FLAMES')),
        fa_file = genome_fa,
        fq_in = fastq1,
        annot = annotation,
        outdir = outdir
    )
}