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Published 20 hours ago • verified publisher icon mlbendall

Annotation for mouse (mm10)?

Open YiweiNiu opened this issue 4 years ago • 3 comments

Hi,

Thanks for developing this useful tool! I got two questions about using telescope:

  1. How to prepare a reference GTF for mm10? telescope_annotation_db does not include a TE reference for mm10.
  2. Was telescope designed only for HERV? I wonder whether it could be applied to other TE class?

Thanks, Yiwei

YiweiNiu avatar Jan 20 '21 07:01 YiweiNiu

@mlbendall Is there any update on this issue? I would be interested in using this tool with mouse data as well.

skchronicles avatar Oct 14 '22 18:10 skchronicles

+1

biomesser avatar Apr 11 '23 13:04 biomesser

Hey,

It is maybe to late, but I created a GTF annotation of transposable elements for mm10, as telescope was part of my tool benchmark (https://academic.oup.com/bib/article/23/1/bbab417/6400501). You can find the annotation here https://zenodo.org/records/4561751 .

Best,

Robert

roschwarz avatar Mar 26 '24 17:03 roschwarz