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Minimap2 re-align reads to transcriptome

Source: R/minimap2_align.R
minimap2_realign.Rd

Uses minimap2 to re-align reads to transcriptome

Usage

minimap2_realign(
  config,
  fq_in,
  outdir,
  minimap2,
  samtools = NULL,
  prefix = NULL,
  threads = 1
)

Arguments

config

Parsed list of FLAMES config file

fq_in

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

outdir

Output folder

minimap2

Path to minimap2 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_align()]

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"))))) {
    fasta <- annotation_to_fasta(annotation, genome_fa, outdir)
    minimap2_realign(
        config = jsonlite::fromJSON(system.file('extdata/SIRV_config_default.json', package = 'FLAMES')),
        fq_in = fastq1,
        outdir = outdir
    )
}