GTF repeatmasker annotation file
I am trying to find an annotation file generated with RepeatMasker through UCSC table browser, but all the GTF files I found only contain repeat sequences associated to exons, andI do not know why. In my case, I want to use a GTF file that contains all repetitive sequences along the genome. Does anyone know where can I find it or how can I solve this problem?
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rfran010 •
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frarodmar17 •
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frarodmar17 •
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Are you referring to the third column "exon". That is a placeholder of sorts. You can check a couple loci manually to confirm they don't align strictly to mRNA exons.
I would also recommend the Hammell Lab's curated GTF files:
https://www.dropbox.com/scl/fo/jdpgn6fl8ngd3th3zebap/ACdZkShDC1au-OckIipI5kM/TEtranscripts/TE_GTF?rlkey=41oz6ppggy82uha5i3yo1rnlx&e=1&subfolder_nav_tracking=1&dl=0