This repository contains code used for quality control and data analysis presented in:

Lee I, Rasoul B, Holub AS, Lejeune A, Enke RA, Timp W. Whole genome DNA methylation sequencing of the chicken retina, cornea and brain. Scientific Data 2017. available at the following URL

---

Data availability

Data is available in NCBI BioProject under the accession number [PRJNA389197] URL here: https://www.ncbi.nlm.nih.gov/bioproject/389197

Software used

Software	Version	URL
Trim Galore!	0.4.1	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Bismark	0.16.3	http://www.bioinformatics.babraham.ac.uk/projects/bismark/
bsseq	1.12.1	https://bioconductor.org/packages/release/bioc/html/bsseq.html

Data analysis code

Code used for all of the quality assessment and data analysis steps are available in each of the scripts below.

1. Quality assessment
2. Adaptor and end-trimming with Trim Galore!
3. Alignment with Bismark
4. Methylation bias plotting
5. Methylation Analysis