no exon lines in the GTF file

[Janet]

Hi,

I am trying to do STAR indexing of my reference genome (only including 72 contigs from NCBI). I downloaded a gbff file from NCBI as well. I converted gbff to GTF with a python script. But there are no exon lines in the GTF file, only gene and CDS lines. So I got the error message "no exon lines in the GTF file".

My reference is only assembled into contigs, and annotated into proteins. I do no have any other information. So my questions are:

1) can STAR consider CDS lines? If not, can I simply replace CDS to exon in my GTF file?

1) If still no, can I use STAR at all? I would like to generate a gene table where the numbers of reads mapped to reference genes are presented.

Thank you!

Best,

Janet

[Janet]

I attached my reference genome and gtf files here for your information. Thanks!

-Janet

[Alexander Dobin]

Hi Janet,

you can rename the "CDS" into "exon", or you can use --sjdbGTFfeatureExon CDS option to tell STAR that your exons are called "CDS".

When converting GFF to GTF, please make sure that each of the CDS lines has the "transcript_id" and "gene_id" tags.

Cheers

Alex

[Janet]

Hi Alex,

It works very well! Thank you!

Best,

Janet