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

READMESummary of all files in this Dryad packageFileS4 NewScaffoldOrder.csvRevised 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.FileS5 revisedAssemblyUnmasked.fa.zipFasta 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.FileS6 revisedAssemblyMasked.fa.zipRepeat 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.FileS7 ensGene_revised.gtfRevised .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.ScafKeyForNewFasta.csvKey for scaffold order in fasta filesSampleList.csvList of all samples and barcodes in the GBS F2s.convertCoordinate.RThis 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.