FLAMES Transcript quantification

Calculate the transcript count matrix by parsing the re-alignment file.

Usage

quantify_transcript_flames(
  annotation,
  outdir,
  config,
  pipeline = "sc_single_sample",
  samples
)

Arguments

annotation

The file path to the annotation file in GFF3 format

outdir

The path to directory to store all output files.

config

Parsed FLAMES configurations.

pipeline

The pipeline type as a character string, either sc_single_sample (single-cell, single-sample),

samples

A vector of sample names, required for sc_multi_sample pipeline. bulk (bulk, single or multi-sample), or sc_multi_sample (single-cell, multiple samples)

Value

A SingleCellExperiment object for single-cell pipeline, a list of SingleCellExperiment objects for multi-sample pipeline, or a SummarizedExperiment object for bulk pipeline.

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)
fasta <- annotation_to_fasta(annotation, genome_fa, outdir)
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> Warning: The "phase" metadata column contains non-NA values for features of type
#>   exon. This information was ignored.
#> OK
config <- jsonlite::fromJSON(create_config(outdir, bambu_isoform_identification = TRUE, min_tr_coverage = 0.1, min_read_coverage = 0.1, min_sup_cnt = 1))
#> Writing configuration parameters to:  /tmp/RtmpoS7Kzz/file1f6d36c84b3a/config_file_8045.json 
file.copy(annotation, file.path(outdir, "isoform_annotated.gtf"))
#> [1] TRUE
if (FALSE) { # \dontrun{
if (!any(is.na(find_bin(c("minimap2", "k8"))))) {
  minimap2_realign(
    config = config, outdir = outdir,
    fq_in = fastq1
  )
  quantify_transcript_flames(annotation, outdir, config, pipeline = "bulk")
}
} # }