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Isoform identification

Source: R/find_isoform.R
find_isoform.Rd

Long-read isoform identification with FLAMES or bambu.

Usage

find_isoform(annotation, genome_fa, genome_bam, outdir, config)

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.