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mhammell-laboratory / TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
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TE GTF for non-model species #209

Open canyon-hub opened 2 weeks ago

canyon-hub commented 2 weeks ago

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 commented 2 weeks ago

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 commented 4 days ago

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 commented 4 days ago

HI,

The alignment score is not essential for the TE GTF.

Thanks.