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mhammell-laboratory / TElocal

A package for quantifying transposable elements at a locus level for RNAseq datasets.
GNU General Public License v3.0
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Zebrafish index for TElocal #11

Closed stefaniehoho closed 3 years ago

stefaniehoho commented 3 years ago

Hi,

I'm very interested to try TElocal for my zebrafish RNAseq data. However, the TElocal index for zebrafish is not available. I'm wondering if I could ask your help in generating Zv10/GRC10 index.

Thank you very much.

olivertam commented 3 years ago

Hi,

Thank you for your interest in the software. We'll start building it, and let you know when it is ready to download.

Thanks.

olivertam commented 3 years ago

Hi,

Sorry for the slow response. A pre-built index of the DanRer10 is ready for download. The GTF that was used to generate this is available here.

Please check that the chromosome IDs between the GTF and your genome build matches up, and let us know if that's not the genome build that you're using.

Thanks.

stefaniehoho commented 3 years ago

Thank you so much for generating this index.

I will download and try it out. Will let you know if it works.

Much appreciated.

wushyer commented 2 years ago

Hi, I want to use this software in another plant. How to build TE index? I already curated the TE gtf files. Thanks

olivertam commented 2 years ago

Hi,

I will address your question here.

Thanks.