This repository contains scripts to preprocess bisulfite sequencing datasets of WT plants and some epigenetic mutants in Arabidopsis thaliana.

1. WT replicate 1 (GSM1242401)

2. WT replicate 2 (GSM980986)

3. met1-3 (GSM981031)

4. drm12cmt23/ddcc (GSM1242404)

5. cmt23 (GSM1242402)

6. suvh4/5/6 (GSM981060)

7. cmt3 (GSM981003)

8. cmt2 (GSM981002)

9. suvh4/kyp (GSM981057)

10. drm1/2 (GSM981015)

11. ibm1 (GSM981026)

Systems requirements

To run the scripts, you will need to have the following programs installed

1. Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/)

2. Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)

3. samtools (http://www.htslib.org/)

4. genomeCoverageBed (http://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html)

To perform the entire preprocessing you need to run preprocess_data.sh script in data directory.

$ cd data

$ chmod +x *.sh

$ ./preprocess_data.sh