ExtractTranscriptomeSequence {nearBynding} | R Documentation |
Writes a FASTA file of transcript sequences from a list of transcripts.
ExtractTranscriptomeSequence( transcript_list, ref_genome, genome_gtf, RNA_fragment = "exon", exome_prefix = "exome" )
transcript_list |
A vector of transcript names that represent the most expressed isoform of their respective genes and correspond to GTF annotation names. Required |
ref_genome |
The name of the reference genome FASTA from which exome sequences will be derived; a string. Required |
genome_gtf |
The name of the GTF/GFF file that contains all exome annotations; a string. Coordinates must match the file input for the ref_genome parameter. Required |
RNA_fragment |
A string of RNA component of interest. Options depend on the gtf file but often include "gene", "transcript", "exon", "CDS", "five_prime_utr", and/or "three_prime_utr". Default "exon" for the whole exome. |
exome_prefix |
A string to add to the prefix for all output files. Default "exome" |
writes FASTA file of transcriptome sequences into directory
transcript_list, genome_gtf, and RNA_fragment arguments should be the same as GenomeMappingToChainFile function arguments
## load transcript list load(system.file("extdata/transcript_list.Rda", package="nearBynding")) ##get GTF file gtf<-system.file("extdata/Homo_sapiens.GRCh38.chr4&5.gtf", package="nearBynding") ExtractTranscriptomeSequence(transcript_list = transcript_list, ref_genome = "Homo_sapiens.GRCh38.dna.primary_assembly.fa", genome_gtf = gtf, RNA_fragment = "three_prime_utr", exome_prefix = "chr4and5_3UTR")