Graphing and tabulating next-generation sequencing and genotyping data

Gilks, William (2016) Graphing and tabulating next-generation sequencing and genotyping data. [Dataset]

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Abstract

Making figures and tables for publication. Each zip archive contains input data, shell script to initiate and log R script, one R script for generating several graphs and tables, and the output graphs and tables themselves.

Data was generated by whole-genome resequencing of 22 individual D.melanogaster from Sussex-LHM population and 2 from the Sussex RG line, followed by read-mapping, then genotyping with Haplotype Caller and Genomestrip.

Locations for raw data, code, logs, extended QC data:

Sequence reads NCBI SRA268956

NCBI dbSNP https://www.ncbi.nlm.nih.gov/projects/SNP/snp_viewBatch.cgi?sbid=1062461

NCBI dbVar accession number pre-release nstd134

The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554

Item Type: Dataset
Additional Information: DOI:10.5281/zenodo.160539
Keywords: Genetics, data visualisation, R, ggplot, Drosophila, genomics, next-generation sequencing.
Schools and Departments: School of Life Sciences > Evolution, Behaviour and Environment
Subjects: Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0438.4 Special aspects of the subject as a whole, A-Z
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0447 Genes. Alleles. Genome
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0470.A-Z Experimental organisms, A-Z
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0470.A-Z Experimental organisms, A-Z > QH0470.D7 Drosophila
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0460 Mutations
Related URLs:
Depositing User: Dr William Gilks
Date Deposited: 15 Nov 2016 13:08
Last Modified: 15 Nov 2016 13:08
URI: http://sro.sussex.ac.uk/id/eprint/65470
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Project NameSussex Project NumberFunderFunder Ref
2Sexes_1Genome: Sex-specific genetic effects on fitness and human diseaseG0781EUROPEAN UNION2011-STG280632