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2. Sequencing Quality Check
George Pacheco edited this page Jul 27, 2021
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A general sequencing quality check of each plate was performed using FASTQc--v0.11.5 under default options. We considered that all the plates passed this general sequencing quality check.
fastqc ~/data/Pigeons/PBGP/PBGP--GBS_Data/PBGP_1A/PBG_1A-C6H23ANXX_8_fastqc.gz
fastqc ~/data/Pigeons/PBGP/PBGP--GBS_Data/PBGP_1B/PBG_1B-C6GGGANXX_7_fastqc.gz
fastqc ~/data/Pigeons/PBGP/PBGP--GBS_Data/PBGP_2/PBG_2-C6GGGANXX_8_fastqc.gz
fastqc ~/data/Pigeons/PBGP/PBGP--GBS_Data/PBGP_1-2_ReRun/PBG_1-2_ReRun-C7U8CANXX_2_fastqc.gz
- 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