Glazer et al 2015 G3 additional files README This summary FileS4 NewScaffoldOrder.csv 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. FileS5 revisedAssemblyUnmasked.fa.zip 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. FileS6 revisedAssemblyMasked.fa.zip 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. FileS7 ensGene_revised.gtf.zip 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. ScafKeyForNewFasta.csv: Key for scaffold order in fasta files SampleList.csv: List of all samples and barcodes in the GBS F2s. convertCoordinate.R: Function to convert between new and original coordinate systems 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]. Inputs: chr is a number or string (e.g. 1, '1', 'Un') of the starting chromosome. pos is a number of the starting position. direction is either 'old2new' or 'new2old'. scafFile gives the path and file name to the file 'FileS4 NewScaffoldOrder.csv' Output: List of [chromosome, position] of the converted coordinate. Examples: convertCoordinate(3,1538202,'old2new','Path/to/FileS4 NewScaffoldOrder.csv') # same position convertCoordinate('Un',37499024,'old2new','Path/to/FileS4 NewScaffoldOrder.csv') # now on chr 1 convertCoordinate('Un',23343225,'old2new','Path/to/FileS4 NewScaffoldOrder.csv') # now on chr 2 convertCoordinate("1",541084,'old2new','Path/to/FileS4 NewScaffoldOrder.csv') # different location on chr 1 convertCoordinate('1',680442,'new2old','Path/to/FileS4 NewScaffoldOrder.csv') # reverse of previous line convertCoordinate(12,594205,'new2old','Path/to/FileS4 NewScaffoldOrder.csv') # used to be on Un convertCoordinate(1,540083,'old2new','Path/to/FileS4 NewScaffoldOrder.csv') # in between contigs in assembly