problem with GTF file

Question

[arshad1292]

Dear community,

I obtained gff3 file by running repeatmasker with -gff option. Then I converted it into GTF using AGAT tool. Note: I tried using gffread to convert this gff3 into gtf format but it did not work.

Going forward, I used this newly generated gtf file for alignment with STAR but I get the following error:

Fatal INPUT FILE error, no exon lines in the GTF file: datepalm_refGene.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 .

When I looked at the GTF, it contained only transcript and gene in the 3rd column and there was no exon listed there.

How can I fix this formatting issue?

Many thanks,

[Juke34]

If star just needs the exon features You can use a sed command to replace \ttranscript\t by \texon\t

[arshad1292]

Thank you for reply. I did the same but then I got another error shown below:

Fatal INPUT FILE error, no valid exon lines in the GTF file: datepalm_refGene.gtf Solution: check the formatting of the GTF file. Most likely cause is the difference in chromosome naming between GTF and FASTA file.

So it seems like there is difference between FASTA and GFT chromosome names. Actually, my GTF file has no chromosome names at all. First column just contains numbering on each row (11, 11, 13, 13, 13, 14, 14 .............. and so on). I used the same FASTA file to generate GTF by following repleatmodeler and repleatmasker steps.

Any idea how it can be fixed?