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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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gtf used to generate pre-built index? #131

Closed EmersonH2 closed 1 year ago

EmersonH2 commented 1 year ago

Hello,

Would it be possible for you to share the original .gtf you used to generate the pre-built index (https://labshare.cshl.edu/shares/mhammelllab/www-data/TElocal/prebuilt_indices/hg38_rmsk_TE.gtf.locInd.gz)? I assume it was one of these from the RepeatMasker website--which one? Screen Shot 2023-01-16 at 1 39 56 PM

Thank you so much for your help! Emerson

olivertam commented 1 year ago

Hi Emerson,

Thank you for your interest in the software. The original GTF used for the prebuilt index is available here. It is derived from the UCSC repeatMasker output for the hg38 genome. I also want to check whether you are using TElocal or TEtranscripts for your analysis. The prebuilt indices for the two software are not compatible. The one that you linked in your original post is for TElocal, while the TEtranscripts prebuilt index for hg38 is available here

Thanks.

EmersonH2 commented 1 year ago

Thank you so much, Oliver! Yes, I'm working with Telocal--thank you for checking!