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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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Pre-generated TE GTF for GRCm39 Ensembl assembly #138

Closed kcwum closed 1 year ago

kcwum commented 1 year ago

Hi team - I see GRCm38_Ensembl_rmsk_TE.gtf but not an equivalent file for GRCm39. I do see mm10 or mm39_rmsk_TE.gtf. Can you please advise which TE GTF file I should use for data aligned to GRCm39 Ensembl assembly. Thank you!

olivertam commented 1 year ago

Hi,

Thank you for your interest in the software. The TE GTF file for GRCm39 Ensembl assembly is now available here. Please let us know if you encounter any issues.

Thanks

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