search

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
217 stars 29 forks source link

GTF files for macaques, bonobo, and also external index #91

Closed ferygood closed 3 years ago

ferygood commented 3 years ago

Hello Oliver,

I would like to use TEtranscripts to analyze TE in primates. However, I do not find all gtf files I want in the archive. Could you provide TE gtf files for macaques (rheMac10) and bonobo (panPan3)? I also see there is pre-generated hg38 index for speed up the analysis in one of the closed issue. Do you think it is also possible to provide index for Chimpanzee (panTro6), macaques (rheMac10) and bonobo (panPan3)? That would be very nice for running huge sample numbers. Thank you for your time.

Best

olivertam commented 3 years ago

Hi,

The GTF files for rheMac10 and panPan3 should be here, and the pre-built indices for panTro6, rheMac10 and panPan3 should be here. Please let me know if you have trouble finding them, or if they don't work.

Thanks.

ferygood commented 3 years ago

Hello Oliver,

Thank you for your immediate reply, I am able to find these files now. I will let you know if I encounter any problems. Many thanks!

Best