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sjteresi / TE_Density

Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
GNU General Public License v3.0
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Can it be applied to 1Mb windows, instead of gene annotations? #138

Closed lcanesin closed 2 months ago

lcanesin commented 11 months ago

Dear Scott Teresi,

Thanks for the amazing tool. I'm wondering if I can/have to tweak it a little bit to apply the method to fixed 1Mb windows. I want to test if any such window containing chr breaks (when compared to closely related species) are enriched for TEs of any given family/order.

Thanks in advance

sjteresi commented 11 months ago

Here is an edit you can try to make:

Make a "gene" annotation file, but instead of gene coordinates you have the coordinates of your fixed windows. You could name this "gene" "interesting_window_1" and TE Density will treat it like a gene and calculate the values for the location. Basically, edit the gene annotation file to contain the entries that you want TE Density to be calculated around.

Cool project idea!

lcanesin commented 10 months ago

That's great! Gonna try it asap. Thanks!