Commit 5aa5a491 authored by Romain Feron's avatar Romain Feron
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Small polishing of index

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RADSex documentation
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RADSex is a software package to analyze RAD-Sequencing data. It is primarily designed to look for sex signal, but it can be used to compare two populations.
RADSex is a software package to analyze RAD-Sequencing data. It is primarily designed to look for sex signal, but it can be used to compare any two populations.
The core idea of RADSex is to compare presence / absence of non-polymorphic markers between individuals in two populations. In the case of a polygenic RAD-Sequencing marker, each allele is represented as a separate marker, whereas other RAD-Sequencing analysis softwares usually group alleles in a single polymorphic marker. Separating alleles from polymorphic markers enables RADSex to easily detect sex-specific alleles, involving a single simple parameter.
The core idea of RADSex is to compare presence / absence of non-polymorphic markers between individuals in two populations. RADSex does not allow mismatches when grouping reads into markers. This means that each allele in a polyallelic gene is represented as a separate marker, whereas other RAD-Sequencing analysis softwares would usually group these alleles in a single polymorphic marker. Separating alleles from polymorphic markers enables RADSex to easily detect sex-specific alleles, using only minimum coverage of a marker as a parameter.
RADSex uses a dataset of demultiplexed RAD reads to generates a table of coverage for each sequence in each individual. This table is then used to infer information about the type of sex-determination system, identify sex-biased sequences, map the RAD sequences to a reference genome, and recover potential polymorphic sex-biased markers.
The basic input file of RADSex is a dataset of demultiplexed RAD reads. From this dataset, RADSex generates a table of coverage for each sequence in each individual. This table is then used to infer information about the type of sex-determination system, identify sex-biased sequences, map the RAD sequences to a reference genome, and recover potential polymorphic sex-biased markers.
Results from RADSex can be visualized with the `radsex-vis` R package, available here: https://github.com/INRA-LPGP/radsex-vis. The `radsex-vis` R package provides easy-to-use functions to generate powerful visual representations of your data.
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