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Add HS1/T2T as genome reference #109

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slsevilla opened this issue Jan 29, 2024 · 2 comments
Open
2 tasks

Add HS1/T2T as genome reference #109

slsevilla opened this issue Jan 29, 2024 · 2 comments
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@kelly-sovacool @slsevilla
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enhancement New feature or request low priority RENEE RepoName

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@slsevilla
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Feature Request

Add HS1/T2T as a reference genome

  • add to biowulf
  • add to frce
@slsevilla slsevilla added the enhancement New feature or request label Jan 29, 2024
@kopardev kopardev added the RENEE RepoName label Jan 29, 2024
@slsevilla slsevilla self-assigned this Jan 29, 2024
@kopardev
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kopardev commented Feb 8, 2024 •
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Does hs1's latest annotation have more genes (novel or new paralogs) than hg38's latest annotation?

@slsevilla Did you do a TechDev on this? Basically: Take human RNAseq data and:

  • run with hg38 + latest annotation
  • run with hs1 + its annotation
  • do we get more read mappings with hs1?
  • are these new mapping to genic regions?
  • as hs1 has more "low-sequence-complexity" regions than hg38,
    • does it take longer to align to hs1?
    • would this require changes to the alignment parameters?
  • are gene-level raw counts changing significantly?

Has any PI requested hs1 specifically??

@slsevilla
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The PI who originally requested this now wants hg38. Moving this to the backburner.

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@kopardev @kelly-sovacool @slsevilla