GTF file error during mapping with STAR

[mars188]

Dear,

I am trying to do a mapping 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

Do you think there is problem with my GTF? If so, how can I fix it.

Many thanks,

[alexdobin]

Hi @mars188

the GTF file should have "exon" in the 3rd column.

[mars188]

I obtained gff3 file by running repeatmasker with -gff option. Then I converted the gff3 into GTF format using AGAT tool. Note: I also tried gffread tool for this conversion but it did not work (only AGAT worked).

But STAR doesn't accept this GTF as it doesn't contain exon in the 3rd column.

Any idea, how this can be fixed? Please let me know if you have any idea.

Many thanks,

[alexdobin]

Hi @mars188

if each line in your GTF represents exons, then you can simply replace the 3rd column with the "exon".

[mars188]

Dear @alexdobin Thank you for reply. I replaced "transcript" with "exon" in this GTF file but 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?