This workflow is designed to perform differential gene expression (DGE) analysis and other analyses on sequencing data from oviduct tissue and cell culture samples harvested from Western Viviparous (WV) and Eastern Oviparous (EO) Z. vivipara.

The folder structure contains:

01_scripts: scripts for running the analysis as well as preprocessing scripts use to produce the salmon quant data from ONT sequencing run output. All scripts were written by J. L. Smout unless otherwise credited. See script comments for full details of workflow.

02_reference_data: Sample sheet (sample_sheet.csv) contains information on RNA samples relevant to this analysis. Genome annotation (annotation.gff & annotation.gtf), protein (protein.faa) and transcript sequences (transcript.fna and transcript.fasta) for Zootoca vivipara, downloaded from NCBI RefSeq database on 22/11/2023 at 1830 GMT, accession GCF_963506605.1. Functional annotations (eggnog.csv) were computed using eggNOG-mapper v2 (http://eggnog-mapper.embl.de/about) and 

03_salmon: Salmon quant results from various samples sequenced in 2022 and 2023, including oviduct tissue samples relevant to this study, as well as other samples not relevant to this study, organised by run date and barcode number (i.e. 03_salmon/Mon_YY_barcode##/quant.sf).