Sex_biased_gene_expression

Repository for the collected scripts used in study: https://doi.org/10.1101/2021.01.23.427895

DATA

Contains

1. Timema californicum read counts- timema_counts.csv
2. dN/dS estimates- all_stages_dnds.txt
3. Drosophila melanogaster read counts- droso_counts.csv
4. Accession numbers of Timema californicum reads reads- reads_accession_numbers.txt

SCRIPTS

Quality control of the reads (removing adapters, trimming), mapping reads to the genome and counting the reads per gene

1. QC_mapping_counting.sh

To analyze Timema data

Get sex-biased genes and classify genes into categories 2. At the hatchling stage- hatclings_edger.R

3. At the juvenile stage- juveniles_edger.R

4. At the adult stage- adults_edger.R

To make a heatmap of sex-biased genes 5. heatmap_timema.R

To plot dNdS values for different sex- bias gene categories and to statistically compare between gene categories groups

6. DnDs.R

To calculate stage specificity of gene expression (Tau index) for sex-bias categories, and statistics to compare tau values between sex-bias gene categories

7. tau_calculation.R

To analyze Drosophila data

Get sex-biased genes and classify genes into categories

1. At the larval stage- droso_larva_edger.R

2. At the juvenile stage droso_pupa_edger.R

3. At the adult stage- droso_adult_edger.R

To get venn diagram plot of three developemental stages, and to statistically test the intersection

4. droso_venn_diagram.R