I am trying to go from raw reads to counts and then to TPM/TMM values of gene expression for a prokaryotic organism (via mapping the RNA sequencing reads to the reference genome). I have read that an annotation file (gtf or gff3) is needed, and encountered this issue firsthand when STAR threw an error saying that my gtf file doesn't have any exon lines.
My question is, how should I go about this process of mapping reads to counts and then to TPM or TMM, given that I can't find a gtf file with exon lines? I am open to using any of the reputable alignment packages e.g. I've heard of Bowtie2 and STAR. I should mention that the gff3 file does have exon lines, but I can't understand if STAR will be happy to use this file.
The exact error that STAR throws is this:
Fatal INPUT FILE error, no exon lines in the GTF file: /Users/fastq/gtf_file.gtf Solution: check the formatting of the GTF file, it must contain some lines with exon in the 3rd column. Make sure the GTF file is unzipped. If exons are marked with a different word, use --sjdbGTFfeatureExon .