Sex-linked gene identification software tools | RNA sequencing data analysis
Sex-linked genes are genes located on sex chromosomes of an individual. Sex-linked genes defects have implications for human health as they can cause abnormal conditions such as hemophilia, color-blindness, etc. Sex-linked gene identification software tools use RNA-seq and transcriptomic data to identify sex-specific marker sequence in human or species for which there are no existing reference genome.
A probabilistic method that relies on RNA-seq 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). SEX-DETector will also work on genotyping data derived from genome sequencing. In some cases, it might be more efficient to use DNA-seq data instead of RNA-seq data to genotype individuals. It is available as a Galaxy workflow.
Identify sex-specific marker sequences. SEXCMD allows users to (i) design sex-specific marker sequences, (ii) train using a known dataset, and (iii) make an optimal sex marker sequence selection. The pipeline can be run to genome and transcriptome sequencing without aligning next generation sequencing (NGS) reads onto a reference genome but by using tens of sex-specific marker sequences from syntenic regions of the sex chromosomes.
A repository to house the code relevant to the project "Systematic Rational Identification of Sex-Linked Molecular Alterations and Therapies in Cancer." The repository contains R scripts used to process and analyze data and results. In our work, we identify cancer-specific and pan-cancer genomic differences between male and female patients. Then, we use Ingenuity Pathway Analysis (IPA) to discover pathways variably enriched in male and female tumors, lending insight into the biological processes that differ between both sexes. Finally, we use our genomic findings to identify drugs that work well in males, females, or both sexes.
Presents a simple and freely accessible software tool for identification of sex chromosome linked genes in species without an existing reference genome. This pipeline uses custom scripts together with external assembly, mapping and variant calling software. Given the resource-intensive nature of the computation, servers with high capacity are a requirement. Therefore, in order to keep this pipeline easily accessible and reproducible, linkyx was implemented in Galaxy – an open, web-based platform for data-intensive biomedical research.