Creating BED files from GTF annotation file for Nano3p-seq analyses
Create a BED file that contains Exon cordinates
Rscript -- vanilla exons.R < GTF_file > < Label >
# Example
Rscript -- vanilla exons.R zebrafish_chr1.gtf zebrafish
Create a BED file that contains Gene cordinates
Rscript -- vanilla genes.R < GTF_file > < Label >
# Example
Rscript -- vanilla genes.R zebrafish_chr1.gtf zebrafish
Create a BED file that contains all transcript end coordinates
Rscript -- vanilla transcript_ends.R < GTF_file > < Label >
# Example
Rscript -- vanilla transcript_ends.R zebrafish_chr1.gtf zebrafish
Create a BED file that contains miRNA gene cordinates
Rscript -- vanilla mirna_genes.R < GTF_file > < Label >
# Example
Rscript -- vanilla mirna_genes.R zebrafish_chr1.gtf zebrafish
Create a BED file that contains smallRNA gene cordinates
Rscript -- vanilla smallrna_genes.R < GTF_file > < Label >
# Example
Rscript -- vanilla smallrna_genes.R zebrafish_chr1.gtf zebrafish
Create a BED file that contains smallRNA transcript end coordinates
Rscript -- vanilla smallrna_transcriptends.R < GTF_file > < Label >
# Example
Rscript -- vanilla smallrna_transcriptends.R zebrafish_chr1.gtf zebrafish