TE GTF for non-model species

[canyon-hub]

Hello,

I’m very excited to use TEtranscripts. However, I work with a non-model genome, and there are no gene and TE annotation files available on your website for this species. Would it be possible for me to create the necessary files on my own? I currently have TE annotations generated by RepeatMasker.

I look forward to your response!

Thank you very much.
canyon

[olivertam]

Hi,

Thank you for your interest in the software.
You can use the following script to process the RepeatMasker output to a TE GTF annotation.
Let us know if you encounter any issues, and we can try to help and troubleshoot.

Thanks.

[liuniba]

Thank you for your reply. My RepeatMasker output is in .gff format, which lacks the alignment score column. Would the absence of alignment scores significantly impact the results? I'm looking forward to your response!

[olivertam]

HI,

The alignment score is not essential for the TE GTF.

Thanks.

[github-actions]

This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days