Transcript quantification — quantify

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

Usage

quantify_transcript(annotation, outdir, config, pipeline = "sc_single_sample")

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), bulk (bulk, single or multi-sample), or sc_multi_sample (single-cell, multiple samples)

Value

The count matrix will be saved in the output folder as transcript_count.csv.gz.

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/Rtmpg58CKQ/file1a585b524993/config_file_6744.json 
file.copy(annotation, file.path(outdir, "isoform_annotated.gtf"))
#> [1] TRUE
if (FALSE) { # \dontrun{
if (!any(is.na(sys_which(c("minimap2", "k8"))))) {
    minimap2_realign(
        config = config, outdir = outdir,
        fq_in = fastq1
    )
    quantify_transcript(annotation, outdir, config, pipeline = "bulk")
}
} # }