/A_thaliana_epigenetic_mutants

Primary LanguageShellGNU General Public License v3.0GPL-3.0

A_thaliana_epigeneitc_mutants

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