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Investigate HiTE #86

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GallVp opened this issue Nov 6, 2024 · 2 comments
Open

Investigate HiTE #86

GallVp opened this issue Nov 6, 2024 · 2 comments
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enhancement New feature or request

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@GallVp
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GallVp commented Nov 6, 2024

Description of feature

GitHub: https://github.com/CSU-KangHu/HiTE
@GallVp GallVp added the enhancement New feature or request label Nov 6, 2024
@GallVp GallVp self-assigned this Nov 6, 2024
@GallVp
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GallVp commented Nov 6, 2024

From Yasin,

  • Asked Katrina about masking and she strongly suggested soft masking the genome.
  • Is HiTE enough for TE masking?
  • Can we directly use the EDTA masked genome instead of running RepeatMasker after EDTA?
  • Can we process input genomes with EDTA to curate a panTE library and report the stats?
  • Different modes of the pipeline and use Helixer for fast mode? Then, why not BRAKER ab initio?
  • Use python scripts to do pangene analysis.

@CeciliaDeng
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As far as I remember, EDTA hard masked the genome, while AUGUSTUS/Braker developers recommended soft-masking

@GallVp GallVp removed their assignment Nov 20, 2024
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@CeciliaDeng @GallVp