This repository contains scripts to preprocess bisulfite sequencing datasets of WT plants and some epigenetic mutants in Arabidopsis thaliana.
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WT replicate 1 (GSM1242401)
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WT replicate 2 (GSM980986)
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met1-3 (GSM981031)
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drm12cmt23/ddcc (GSM1242404)
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cmt23 (GSM1242402)
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suvh4/5/6 (GSM981060)
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cmt3 (GSM981003)
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cmt2 (GSM981002)
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suvh4/kyp (GSM981057)
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drm1/2 (GSM981015)
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ibm1 (GSM981026)
Systems requirements
To run the scripts, you will need to have the following programs installed
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Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/)
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Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
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samtools (http://www.htslib.org/)
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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