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), orsc_multi_sample
(single-cell, multiple samples)