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Overview

SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes located on the non recombining part of sex chromosomes).

How does SEX-DETector work ?

SEX-DETector does not require prior sequencing of a reference genome : the same sequencing data can be used for the assembly and for the mapping of the reads. A full documentation on the pipeline can be found here.

  • we recommend Trinity for the assembly.
  • Trinity components should be merged with cap3. Our code to perform the merging is available here.
  • We recommend BWA for mapping of the reads.
  • When the mapping has been perfomed, the individuals need to be genotyped ; SEX-DETector takes files produced by Reads2snp (which is available for download on the PopPhyl website) as input.

Here’s a sketch of the entire pipeline (click to open a pdf) :

PNG - 30.4 ko
SEX-DETector pipeline
Schematic pipeline of a typical SEX-DETector analysis.

SEX-DETector can be used as a stand-alone application (download the source code here). You can also use SEX-DETector on a Galaxy server ; you can find more details here.

Contributions

SEX-DETector was developed by Aline Muyle (LBBE).
The Galaxy workflow and wrappers for SEX-DETector were developed by Jos Käfer (LBBE). Khalid Belkhir (PopPhyl project, Montpellier) kindly provided and adapted wrappers for upstream steps of the pipeline.