Long-read isoform identification with FLAMES or bambu.
Arguments
- annotation
Path to annotation file. If configured to use bambu, the annotation must be provided as GTF file.
- genome_fa
The file path to genome fasta file.
- genome_bam
File path to BAM alignment file. Multiple files could be provided.
- outdir
The path to directory to store all output files.
- config
Parsed FLAMES configurations.
Value
The updated annotation and the transcriptome assembly will be saved in the
output folder as isoform_annotated.gff3 (GTF if bambu is selected) and
transcript_assembly.fa respectively.
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)
config <- jsonlite::fromJSON(
system.file("extdata", "config_sclr_nanopore_3end.json", package = "FLAMES")
)
minimap2_align(
config = config,
fa_file = genome_fa,
fq_in = fastq1,
annot = annotation,
outdir = outdir
)
#> 02:13:19 AM Fri Oct 25 2024 minimap2_align
#> total mapped primary
#> /tmp/RtmpoS7Kzz/file1f6d501e647a/align2genome.bam 2503 1772 2500
#> secondary
#> /tmp/RtmpoS7Kzz/file1f6d501e647a/align2genome.bam 0
if (FALSE) { # \dontrun{
find_isoform(
annotation = annotation, genome_fa = genome_fa,
genome_bam = file.path(outdir, "align2genome.bam"),
outdir = outdir, config = config
)
} # }