Code for the crb2a multi omics manuscript
This is the analysis pipeline for the DNA methylation analysis and integration of RNA-seq and methylation (RRBS) data for the manuscript :
Loss of the crumbs cell polarity complex disrupts epigenetic transcriptional control and cell cycle progression in the developing retina
Owen, N., Toms, M., Tian, Y., Toualbi, L., Richardson, R., Young, R., Tracey-White, D., Dhami, P., Beck, S., Moosajee, M.
Journal of Pathology 2023 Apr;259(4):441-454. doi: 10.1002/path.6056
The code is organised for reviewers and reseachers to validate our analysis result. The RRBS data was generated from control (wt) and crb2a-/- zebrafish at 56 hpf. The raw NuGen generated bcl file are taken as input. The process of data analysis has been outlined in the following numbered section, indicating the sequence of analysis. Input for subsequent sections often requires results from the formal analysis.
In each folder, there is a R script called main.R, by running it in R session, in theory all results presented in this repo could be reproduced. Users need to install corresponding R packages, install corresponding R version (4.0.2+).
All analysis within are using Ensembl genome as genomic annotation (version 98), except for CpG islands information used in ./05_GlobalIntegration, which is downloaded from USCS.
The raw data for both RNA-seq and RRBS has been depositied within the NCBI Gene Expression Omnibus (GEO) at GSE178709 and GSE178842