/steelhead_siletz_RNAseq

Primary LanguageShellMIT LicenseMIT

Siletz River RNAseq

Project description

This project examines the genetic effects of a hatchery on Siletz River steelhead (Oncorhynchus mykiss). We performed a series of crosses on adult first-generation hatchery-origin and natural-origin steelhead and conducted RNA-Seq on 120 offspring that we reared in a common garden environment. Information for all sequenced offpsring can be found in Table 1.

Corresponding article [place holder for citation]

Scripts

Code for the project are split up into directories:

  1. alignment_and_sorting. bash scripts for alignment of raw reads
  2. featureCounts. count transcripts
  3. DEGs. identify DEGs in main and reciprocal crosses
  4. maternal_effects. evaluate maternal effects

Data

All raw data and sample metadata generated for this project are stored in the NCBI Short Read Archive (SRA) under project PRJNAXXXX (link pending).