Scripts to:

1. mask C/T polymorphisms in BSseq data
2. process genome and annotation to identify:
   • transcriptional start sites (TSS)
   • promoter regions
   • CpG islands and shores
3. test for differential methylation using R packages "DSS" and "dmrseq"

bedtools: https://bedtools.readthedocs.io/en/latest/
R: https://www.r-project.org/
DSS: http://bioconductor.org/packages/release/bioc/html/DSS.html

Optional:
dmrseq: http://bioconductor.org/packages/release/bioc/html/DSS.html
EMBOSS: http://emboss.sourceforge.net/index.html

• Reference genome or reference sequences in fasta format (required)
• Gene annotation information in GFF format (only required for creating accessory BED files)
• BSseq results in bedGraph format (similar to that output by Bismark or MethylDackel)
• BED file of C/T and A/G SNP polymorphisms

1. Copy or download the genome in fasta format into the ./02_reference folder and rename it "genome.fasta"

2. Optional: Copy or download the gene annotation into the ./02_reference folder and rename it "genes.gff" (can be gzipped)

3. a) Copy bedGraph files (gzipped) into the ./03_raw_bedGraphs folder and execute ./01_scripts/01_remove_CT_SNPs_from_bedGraphs.sh

OR

3. b) Place analysis ready bedGraph files (gzipped)into the ./04_filtered_bedGraphs folder

4. Create sample information file (a script to make a crude file based on the available bedGraphs is found in the ./01_scripts/util/ directory)

5. Create a copy of the ./config.yml file and adjust the parameters to suit your analysis

6. Execute scripts of interest and collect results

Kyle Wellband - kyle.wellband [at] gmail.com

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methylUtil by Kyle Wellband is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.