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Manual Pangenome #40

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nselem opened this issue Apr 25, 2023 · 3 comments
Closed

Manual Pangenome #40

nselem opened this issue Apr 25, 2023 · 3 comments
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@HaydeePeruyero @Czirion

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@nselem
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nselem commented Apr 25, 2023

Develop episode 04-manual-pangenomes.md to explain the two-step process, you need a distance plus a clustering algorithm to calculate pangenomes. Chose a reduced-size example that runs in live-coding, some genomes, or some gene families making sure you exemplify core/shell and cloud genome. Faa files from annotations should be used.
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@nselem nselem added this to the 05/05/2023 milestone Apr 25, 2023
@HaydeePeruyero
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Extraer familias para hacer un blast pequeño. Hacer las comparaciones de todos los genes contra todos los genes.

@Czirion Czirion modified the milestones: First deaft manual pangenome, first draft May 19, 2023
@Czirion Czirion mentioned this issue May 19, 2023
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@HaydeePeruyero
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Families with bdbh algorithm

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Czirion commented May 26, 2023 •
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The code is ready!

  • Review the text of first two sections
  • Review the text of third section
  • Add an exercise

Major issue

  • Consider a similarity threshold in the BDBH algorithm

@Czirion Czirion self-assigned this May 26, 2023
@Czirion Czirion modified the milestones: First deaft manual pangenome, Episodio listo para correr Jun 2, 2023
@Czirion Czirion closed this as completed Sep 22, 2023
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@nselem @HaydeePeruyero @Czirion