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annotation_building

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