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# MicrobiomeComparison
The aim of this project is to compare the tomato microbiome data from all projects generated in the lab (amplicon sequencing and culture collection data).
This will help us better understand how stable tomato microbiome is and which taxa are most prevalent regardless of the experimental condition, year of experiment or plant genotype. Furthermore, shotgun metagenomics data can be integrated to predict functional potential of them.
## 16S amplicon data
In all cases following primers were used:
- 341F= CCTACGGGNGGCWGCAG (V3)
- 785R= GACTACHVGGGTATCTAATCC (V4)
#### Tomato field studies (Stalin)
```
/data/ngs/ME/raaijmakers_group/Ecuador_Tomato_2019/raw_sequences/16S
/data/ngs/ME/raaijmakers_group/Ecuador_Tomato_2019/Tiputini_and_Quito/raw_sequences/16S
```
#### Tomato genotype study (Stalin)
```
/data/ngs/ME/raaijmakers_group/RIL2019_raw/RIL2019_raw_16S_18S/renamed/
```
Sequencing files are stored within the RIL study folder. All files starting with letters belong to this study.
#### RIL study (Ben)
```
/data/ngs/ME/raaijmakers_group/RIL2019_raw/RIL2018_raw_16S_18S/raw_sequences
/data/ngs/ME/raaijmakers_group/RIL2019_raw/RIL2019_raw_16S_18S/renamed/
```
The 2018 had issues of batch effect and was not used for QTL analysis.
#### Successive planting study (Viviane)
__Publication: [STOTEN, 2021](https://www.sciencedirect.com/science/article/pii/S0048969720383583)__
```
/mnt/nfs/bioinfdata/ngs2/ME2/raaijmakers_group/vivianec/BaseClear_16S_amplicon_sequencing_cycling/2019/raw
```
### Seed microbiome (Victor)
```
/mnt/nfs/bioinfdata/ngs2/ME2/raaijmakers_group/B2R-project/victorc/2017.07.13trial_blockers_seeds/amplicon-project/data
/mnt/nfs/bioinfdata/ngs2/ME2/raaijmakers_group/B2R-project/victorc/seed_sperm_rhizo_DNA_RNA/amplicon-project/data
```
/seed_sperm_rhizo_rna_dna_christina/SSPRRH/ # "pool" represents RNA samples
/seed_sperm_rhizo_gisell/data
Map file for this work is located at following location: /mnt/nfs/bioinfdata/ngs2/ME2/raaijmakers_group/B2R-project/victorc/seed_sperm_rhizo_DNA_RNA/amplicon-project/data.
## Culture collection data
#### RIL population study
```
/home/NIOO.INT/beno/16S_sanger_sequencing/data/short_assembled.with.headers.fasta
```
#### WT and monyemaker, rhizosphere Vs endosphere (Victor/Viviane)
```
/mnt/nfs/bioinfdata/ngs2/ME2/raaijmakers_group/B2R-project/victorc/collection_isolates_sanger_seq/Vic_Vivi_B2R_tomato/2017.10.31_Hannah_rhizosphere
/mnt/nfs/bioinfdata/ngs2/ME2/raaijmakers_group/B2R-project/victorc/collection_isolates_sanger_seq/Vic_Vivi_B2R_tomato/all_tomato.fasta
```
File `result_file.fasta` contains merged forward and reverse reads and `taxonomy.txt` their classification (RDP classifier).
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