How to generate GTF file ?

Question

[sunnykevin97]

HI

The non-model organism I'm working has as only primary assembly available with 25 + mtDNA = 26 replicons. The unplaced scaffold information was missing. I assembled RNA_seq data using de novo pipelines, for the assembly evaluation purpose and further downstream analysis I need to have GTF file. How do I generate this file ? Suggestions please.

Thanks

Answer 1

[lieven.sterck]

if you are looking for a GTF file holding the gene annotations, you will have to do genome annotation first (and this is unfortunately not an easy nor straightforward process). If it's not the gene annotations you need, it might be feasible to reformat files you have to be GTF compliant (Keep in mind that GTF is a tricky and difficult format, if it's anyhow possible try to go for GFF(3) formats in stead)

[sunnykevin97]

Thanks for suggestions!