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Merge assembled transcripts with TACO

Source: R/05_04_assembly_quantification_stringtie.R
taco_merge.Rd

This function merges GFF files from StringTie assembly into a single GFF.

Usage

taco_merge(
  sample_info = NULL,
  stringtiedir = "results/05_quantification/stringtie",
  threads = 1
)

Arguments

sample_info

Data frame of sample metadata created with the function create_sample_info.

stringtiedir

Directory where StringTie output files will be stored.

threads

Number of threads to use. Default: 1.

Value

A 2-column data frame with the TACO run status, with "OK" if the program merged transcripts successfully, and NA otherwise.

Details

The GFF files for each BioSample are first merged into BioProject-level GFF files. Then, these Bioproject-level GFF files are merged into a single file that represents the whole set.

Examples

data(sample_info)
qc_table <- summary_stats_fastp(system.file("extdata", package = "bears"))
mappingdir <- system.file("extdata", package="bears")
gff_path <- system.file("extdata", "Homo_sapiens.GRCh37.75_subset.gtf",
                        package="bears")
stringtiedir <- tempdir()
if(stringtie_is_installed()) {
    a <- stringtie_assemble(sample_info, qc_table, mappingdir, 
                            gff_path, stringtiedir)
}
if(taco_is_installed()) {
    taco_merge(sample_info, stringtiedir)
}