Differential expression in the retina of rainbow trout exposed to a magnetic pulse

The code for analysis of the trout retina RNA-seq data. The results from the following analyses are published in:

Fitak RR, Schweikert LE, Wheeler BR, Ernst DA, Lohmann KJ, and Johnsen S. (2018) Near absence of differential gene expression in the retina of rainbow trout after exposure to a magnetic pulse: Implications for magnetoreception. Biology Letters. 14(6): 20180209. doi: 10.1098/rsbl.2018.0209

The raw sequences have been deposited into the NCBI short read archive (SRA): BioProject PRJNA391176

Additional data for this study can be found in: Fitak R, Schweikert L, Wheeler B, Ernst D, Lohmann K, Johnsen S (2018) Data from: Near absence of differential gene expression in the retina of rainbow trout after exposure to a magnetic pulse: implications for magnetoreception. Dryad Digital Repository. https://doi.org/10.5061/dryad.24732

The outline and associated code are found below:

1. Trim the raw sequencing data
2. Download and prepare the reference genome and annotations
3. Index the reference genome
4. Map trimmed reads to reference
   • Calculate summary mapping statistics
5. Verify quantification with STAR and HTSeq
6. Differential Expression using DESEQ2
7. Assembly and quantification in CUFFLINKS
8. Analysis of the CUFFLINKS reference annotation-based transcript (RABT) assembly
9. Various plotting code and functions