I wanted to Generate genome indexes using a tool called STAR, this requires reference genome sequences (FASTA files) and annotations (GTF file), when I launched STAR a message popped up:
Fatal INPUT FILE error, no valid exon lines in the GTF file: /content/drive/MyDrive/gencode.v34.annotation.gtf Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.
So I checked chromosome naming and found that chromosomes in the reference genome are named [chromosome 1] and in the GTF file they are named [chr1], so thought to change chromosomes naming in the reference genome using this code:
But when I check the document I found them unchanged:
Just wanted to know what I'm doing wrong.