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81-A1Meetings.Rmd
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81-A1Meetings.Rmd
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# (APPENDIX) Appendix {-}
# Appendix 1: Meetings
## 11/02/2021 Sylvain's Kick-off
*NT, MH, & SS*
### Funding
* GPR (labex COTE + idex UB): audition 01/21, answer 03-06/21
* Currently enough for __2__ species this year
### Site
* __Regina__
* 1 LiDAR in 2016 (ONF, see Fig. \@ref(fig:reginaMap) and Fig. \@ref(fig:\@ref(fig:reginaMap)))
* Possibility of clearing for drone
* Destructive sampling for tree rings? Coring individuals. **Ask ONF.**
* Higher trees. Maybe not older but at least implying more cell divisions regarding mutations.
* __Paracou__
* 4 LiDAR campaigns from 2004 to 2015 (Fig. \@ref(fig:paracouMap))
* Proximity, easier to follow phenology and collect flowers and fruits
### Species
1. *Dicorynia guyanensis*
1. ...
1. *Eschweilera sp*
* _Sextonia rubra_:
* already sampled
* Paracou
* _Dicorynia_:
* Paracou & Regina
* flowering time? **Ask Natalia Norden and Jerome Chave for original data + Patrick Heuret for his shared article**
* Suggestion: spot one already flowering before sampling
* Check the phenology at the herbarium
* _Eschwerilera sp_:
* Parcou (small) and Regina (big)
* _Handoranthus sp_:
* published genosegmenmes (to read) but high variation
* Regina
* Need to be collected for flux cytometry
* _Caryocar sp_:
* Paracou (big)
* many lianas
* no self shading?
### Field work
* __Regina__
* beginning of march
* wood samples
* drone
* dry leaves of *Handoranthus sp* for flux cytometry from our favorite individuals and two other potential candidates
* Sample (Big shot) *Eschweilera sp* for identification and gene pool attribution with Myriam's SSRseq experiment (results in spring)
* __Paracou__
* _Dycorinia_ from interplots. **Ask Partick Heuret and Eric Nicolini.**
### Genomics
* Check flux cytometry confidence: plot second against first sampling for confidence envelope (Fig. \@ref(fig:fluxconfidence))
* choose what to sequence
* get in touch asap sequencing company
* High molecular DNA extraction at CNRGV
* Bionano with CNRGV
* PacBio for HiFi reads
## 27/05/2021 William Marrande
### Sampling
* No experience on cambium
* PacBio 50-150kb < Bionano
* CTAB or Kit
* Send by plane
### Assembly
* PacBio HiFi best contiguity
* hifiasm separate haplophase
* different apporaches for optical map
* calssical assembly with bionano software (only 3% of N recently)
* if issues (gaps or N), local tools to make it better
## 06/07/2021 Mutation detection
### Virtual experiment
* Barplot of callers performance across AF at low (50X) and high (100X) coverage
* Check `VarScan` AF=0.1 C=200
### Swiss data
* Map swiss mutations (+1000 bp) on 3P genome
* Compare GATK/Strelka2
* Full genome
* Stringent filters common with both GATK and Strelka2
### Angela
*
## 21/01/2022 Mid-project meeting
### Notes
* UVs can have a different signal than direct light exposure measured by Accupar or currently modeled with lidar data (up to 20-30% uncertainty according to G. Vincent)
* lidar gave a hieght of 50.6m against 51.25 with tree climbing. This erros below the meter is very encouraging.
* *Herrera CM 2019* on the phenotypic variability within individual trees or plants
* Screwdriver can be good to initiate the auger (O. Martin)
### Follow-up
* **Branch dating**
* discuss with Patrick and perhaps Romain methodology, sampling points, tools etc
* plan a mission with climbers
* send samples to Patrick
* **Direct light measurement**: not primordial to do aside from a mission if time
* **Mutation detection**: continue with the plan
* **Offspring genotyping**: meet with geneticists to discuss samples and techniques, dimensions of the assay.
* **Data management**: discuss archiving with everybody, e.g. NCBI for raw genomic data, Zenodo for cleaned genomic data, GitHub for codes, what for the others (lidar) ?
## 10/02 Carrotage
*Patrick, Niklas, moi*
* Jocelyn, Valentine, Patrick, Niklas?, me?, Olivier Brunaux?
* 21-25/03
* 3 days
* Book climbers
* Book 2 cars
* Book accommodation in St-George or Regina
* OM for me, Niklas and Jocelyn
* Material
* carottage => Patrick
* climbing kit, ask Ilo
* Accupar
## 05/05 Sixto's results
*Niklas, Myriam, Thibault, me*
* Globally: don't follow archi, no signal in UVs, and the estimate gives a high # of low AF mutations + evidence the difficulty to estimate mutations # comparing with previous studies
* Next steps: annotation (w transcripts, contact Christophe & Isabelle) & transmission (suggest a number of shared mutations in branches with position in the genome + ranking)
* Meeting: schedule a meeting with everybody to discuss valorisation
* 3 papaers: 2 genomes, 1 mutations
* Save data
* Follow mutations sharing along architecture (cell surfing idea)
* Add architecture when comparing phylogenies
* Add comparisons with oka if possible
## 20-21/03 Mutations days
* Collection Chêne Saint-Malo
* mutasom limitée
* majoritairement neutre
* rare dans la population donc lente à se répandre
* minmap for pangenome graph => Verzy ?
* Karst et al. 2023 overinterpretation myccorhizal
*