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rewrite for clarity
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ahernank committed Oct 11, 2024
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26 changes: 13 additions & 13 deletions _posts/2024-10-02-ag3-cohorts-v20240924.md
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Expand Up @@ -27,18 +27,18 @@ ag3 = malariagen_data.Ag3(

This new version introduces some key changes:

- Samples that were previously assigned as `gcx1`, have been renamed as `bissau`:
- `gcx` stands for `genetic cryptic species`, we use these labels as name placeholders for groups that fall outside our usual taxonomic assignment
- In line with [Caputo et al. (2024)](https://malariagen.github.io/vobs-updates/2024/09/10/caputo.html), which characterises the `gcx1` group, we have updated its proposed name to `Bissau molecular form`
- 291 samples that were previously assigned to the `gcx1` group, are now relabeled as `bissau`.
- 5 samples samples that were previously `unassigned`, are now relabeled as `bissau`.
- these changes also affect cohort names, e.g. `GM-M_gcx1_2019` has now been relabeled to `GM-M_biss_2019`

- 36 samples that were previously `unassigned`, have been renamed as (32) `melas`, (2)`gambiae`, (1) `fontenillei`, (1) `arabiensis`.

- An error on the administrative region 1 metadata has been fixed, affecting 119 samples. Tor these:
- `admin1_iso` has been relabeled from `UG-E` to `KE-04`
- `admin1_name` has been relabeled from `Eastern Region` to `Busia`
- these changes also affect cohort names, e.g. `UG-E_arab_2013` has now been relabeled to `KE-04_arab_2013`
- Samples previously labeled as `gcx1` in the `taxon` field have been renamed to `bissau`:
- `gcx` (`genetic cryptic species`) labels serve as placeholders for groups outside our usual taxonomic assignment
- Following [Caputo et al. (2024)](https://malariagen.github.io/vobs-updates/2024/09/10/caputo.html), the `gcx1` group has been renamed to `Bissau molecular form`
- 291 samples previously assigned as `gcx1`, are now labeled as `bissau`.
- 5 previously `unassigned` samples are also relabeled as `bissau`.
- Cohort names have been updated, e.g. `GM-M_gcx1_2019` is now `GM-M_biss_2019`

- 36 `unassigned` samples have been reclassified as: 32 `melas`, 2`gambiae`, 1 `fontenillei`, 1 `arabiensis`.

- A location metadata error affecting the administrative region (level 1) of 119 samples has been corrected:
- `admin1_iso` updated from `UG-E` to `KE-04`
- `admin1_name` updated from `Eastern Region` to `Busia`
- Cohort names have been updated, e.g. `UG-E_arab_2013` has now been relabeled to `KE-04_arab_2013`

If you need to access the previous version of the cohorts analysis, you can use pin it using the code in [here](https://malariagen.github.io/vobs-updates/2024/07/24/ag3-cohorts-v20240717.html).

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