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

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sr320 opened this issue Mar 10, 2023 · 4 comments
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Develop count matrix for transposable elements (copy number) #4

sr320 opened this issue Mar 10, 2023 · 4 comments
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sr320 commented Mar 10, 2023

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@sr320 sr320 self-assigned this Mar 10, 2023
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sr320 commented Mar 24, 2023 •
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@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
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Need to confirm correct genome to use before we can develop the count matrix

@hputnam
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hputnam commented May 19, 2023

@kubu4 We have chosen the P. meandrina genome.

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kubu4 commented Jun 6, 2023

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

@sr320 sr320 closed this as completed Jun 16, 2023
@kubu4 kubu4 mentioned this issue Oct 10, 2023
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