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1. Data Access
George Pacheco edited this page Aug 16, 2021
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The GBS raw data was directly downloaded from the server of the Institute of Biotechnology — University of Cornell using an ordinary
-wgetcommand. This data is now stored on ERDA under Pacheco's account (DQM353), and can be downloaded through the links below.
| Plate | # of Reads | md5sum |
|---|---|---|
| PBP_1A | 312,104,405 | f74732c1074b97dd35851d7e35382d95 |
| PBP_1B | 134,258,551 | 60cee5b6f15d92f79cb85b84a3f59643 |
| PBP_2 | 278,107,611 | 9b596d6cb4d83c9fff462de2303068fd |
| PBGP_1-2_ReRun | 142,795,395 | 823dfab9cb4a72a75891bb2a5849f727 |
- 1. Data Access
- 2. Sequencing Quality Check
- 3. Demultiplexing
- 4. Creation of Mapping Targets
- 5. Filtering For Chimeric Reads
- 6. GBS Sexing
- 7. Read Processing & Mapping
- 8. Running Stats & Filtering of Bad Samples
- 9. Filtering of Possible Paralogs
- 10. Merging of Duplicate Cases
- 11. Investigation of Filtering of Possible Paralogs
- 12. Creation of Specific Datasets
- 13. Loci Information
- 14. Heterozygosity Calculation
- 15. Population Genetics Statistics
- 16. Phylogenetic Reconstruction
- 17. Multidimensional Scaling
- 18. Estimation of Individual Ancestries
- 19. Inference of Population Splits
- 20. Measuring of Linkage Disequilibrium
- 21. GWAS