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.
Data is available in NCBI BioProject under the accession number [PRJNA389197] URL here: https://www.ncbi.nlm.nih.gov/bioproject/389197
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 |
Code used for all of the quality assessment and data analysis steps are available in each of the scripts below.