TElocal to locate the TE loci

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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TElocal to locate the TE loci #177

Closed songlyzz closed 5 months ago

songlyzz commented 5 months ago

Hi olivertam, I sorry for bother you again, but I have trouble with TElocal and have to ask for your advice. When I use TElocal to find each TE loci, I was confused about the nomenclature for example: X6B_LINE_dup272:X6B_LINE:CR1:LINE, X6B_LINE_dup317:X6B_LINE:CR1:LINE, X6B_LINE_dup336:X6B_LINE:CR1:LINE .... Can I know it's real genome loci on the human genome? or how to disstinguish each TE loci?

Thanks very much!

olivertam commented 5 months ago

Hi,

Thank you for your interest in the TElocal software. You can find the locations for the genomic loci here. The GTF that were used to generate the TElocal indices are the same as the ones used in TEtranscripts (available here), with the instance name in the transcript_id field.

Thanks.