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Develop count matrix for transposable elements (copy number) #4

Closed sr320 closed 1 year ago

sr320 commented 1 year ago

@kubu4 could you run RepeatMasker on Pver genome?

-species "all" : Sets species to all
-gff : Create GFF output file (in addition to default files)
AHuffmyer commented 1 year ago

Need to confirm correct genome to use before we can develop the count matrix

hputnam commented 1 year ago

@kubu4 We have chosen the P. meandrina genome.

kubu4 commented 1 year ago

Repeats GFF is now available! Get it here (13MB):

https://gannet.fish.washington.edu/Atumefaciens/20230526-pmea-repeatmasker-Pocillopora_meandrina_HIv1.assembly/Pocillopora_meandrina_HIv1.assembly.fasta.out.gff