Data from: Genomic characterization of sex-identification markers in Sebastes carnatus and Sebastes chrysomelas rockfishes

Folwer BLS, Buonaccorsi VP

Date Published: December 30, 2015

DOI: http://dx.doi.org/10.5061/dryad.3c8s8

 

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Title batch_7.2.sumstats.tsv
Downloaded 12 times
Description Stacks1.04 populations output provides summary statistics for each locus containing SNPs. To identify sex markers, we split each species into male and female samples: S. chrysomelas males were assigned to Pop 1, S. chrysomelas females were assigned to Pop 2, S. carnatus males were assigned to Pop 3, and S. carnatus females were assigned to Pop 4. See the Stacks manual for headers.
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Title batch_7.catalog.tags.tsv
Downloaded 20 times
Description Stacks1.04 denovo_map.pl pipeline was used to construct a catalog of loci from ddRAD-seq reads of S. carnatus and S. chrysomelas samples. . We specified a minimum depth of coverage (m) of two, a maximum number of mismatches between stacks (alleles) within an individual (M) of two, and a maximum number of mismatches between individuals (n) of one to build the catalog. M and n allow for assembly of polymorphic loci within individuals and fixed differences among individuals at a locus, respectively. See the Stacks manual for headers.
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Title matches.tsv
Downloaded 32 times
Description Samples' stacks are matched to the catalog to create a matches.tsv file for each sample. We counted the matches to the catalog to find the depth of each locus in each individual sample. This file must be unzipped. See the Stacks manual for headers.
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Title Fixed differences
Downloaded 21 times
Description This R script was used to identify loci with SNPs that are differently fixed between males and females (ie all males are heterozygous, all females are homozygous). The loci identified are on the sex chromosomes, but given our parameters they have not diverged enough for Stacks to split them into separate loci. We tested the scrip on loci that mapped to select scaffolds where sex-specific markers were found, and then we applied the script to filter the entire sumstats.tsv file.
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Title Filtering for sex-specific loci
Downloaded 66 times
Description The R script counts each samples' matches (matches.tsv) to the catalog (Batch_7.catalog.tags.tsv) and tabulates the depth of each locus in each individual. We then filtered for presence in all of one sex and none of the other sex. We identified loci present in all males and no females.
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When using this data, please cite the original publication:

Folwer BL, Buonaccorsi VP (2016) Genomic characterization of sex-identification markers in Sebastes carnatus and Sebastes chrysomelas rockfishes. Molecular Ecology 25(10): 2165–2175. http://dx.doi.org/10.1111/mec.13594

Additionally, please cite the Dryad data package:

Folwer BLS, Buonaccorsi VP (2015) Data from: Genomic characterization of sex-identification markers in Sebastes carnatus and Sebastes chrysomelas rockfishes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3c8s8
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