Data from: Genome assembly improvement and mapping convergently evolved skeletal traits in sticklebacks with genotyping-by-sequencing

Glazer AM, Killingbeck EE, Mitros T, Rokhsar DS, Miller CT

Date Published: June 5, 2015

DOI: http://dx.doi.org/10.5061/dryad.q018v

 

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Title README
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Description Summary of all files in this Dryad package
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Title FileS4 NewScaffoldOrder.csv
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Description Revised scaffold order for each chromosome (consensus of FTC and BEPA). Revised coordinates (based on this study) and original assembly coordinates are presented. Orientations are defined relative to original genome assembly. The orientation of some scaffolds was not detected in this study. These scaffolds are labeled as having 'unknown' orientation; their orientation was not altered relative to their orientation in the original genome assembly. Chromosome 'M' is the mitochondrial genome sequence, which was not analyzed in this study but is replicated in the revised genome assembly.
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Title FileS5 revisedAssemblyUnmasked.fa.zip
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Description Fasta file containing revised genome assembly based on consensus scaffold order and orientation as described in File S4 in the Glazer et al. manuscript. File is zipped.
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Title FileS6 revisedAssemblyMasked.fa.zip
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Description Repeat masked fasta file containing revised genome assembly based on consensus scaffold order and orientation as described in File S4 in the Glazer et al. manuscript. Repeat masked fasta file is based off the repeat masked version of the original genome assembly, which was masked with RepeatMasker. File is zipped.
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Title FileS7 ensGene_revised.gtf
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Description Revised .gtf file of Ensembl gene predictions. Coordinates of gene predictions were converted to the revised assembly coordinates. All Ensembl-predicted genes were included, except ENSGACT00000019430, which spans two scaffolds (11 and 79) that are not adjacent in the revised genome assembly. File is zipped.
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Title ScafKeyForNewFasta.csv
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Description Key for scaffold order in fasta files
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Title SampleList.csv
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Description List of all samples and barcodes in the GBS F2s.
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Title convertCoordinate.R
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Description This R function converts between the 'old' and 'new' stickleback assembly coordinate systems. The 'old' coordinate system is the assembly described in the Jones et al 2012 stickleback genome paper. It requires access to the FileS4 NewScaffoldOrder.csv file. It has 4 inputs: chr, pos, direction, and scafFile. It returns a list of [chromosome, position]. See README or comments in convertCoordinate.R for further details.
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When using this data, please cite the original publication:

Glazer AM, Killingbeck EE, Mitros T, Rokhsar DS, Miller CT (2015) Genome assembly improvement and mapping convergently evolved skeletal traits in sticklebacks with genotyping-by-sequencing. G3: Genes - Genomes - Genetics 5(7): 1463-1472. http://dx.doi.org/10.1534/g3.115.017905

Additionally, please cite the Dryad data package:

Glazer AM, Killingbeck EE, Mitros T, Rokhsar DS, Miller CT (2015) Data from: Genome assembly improvement and mapping convergently evolved skeletal traits in sticklebacks with genotyping-by-sequencing. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.q018v
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