I have an incomplete GTF file with lines such as:
chr1 hg38_ct_UserTrack_3545 exon 94353 94355 2109 + . gene_id "R2_66"; transcript_id "R2_66_1";
This describes an exon. All the lines in my incomplete GTF file describe an exon or CDS.
I want to fix my GTF file. For instance, I need to do something like:
chrI hg38_ct_UserTrack_3545 gene 6790136 6808198 . + . gene_id "R1_102";
chrI hg38_ct_UserTrack_3545 transcript 6790136 6808198 . + . transcript_id "R1_102";
I would like to add annotation at the transcript and gene level. What's the best way?