MethylExtract main script (MethylExtract_version.pl) The main script of MethylExtract performs methylation profiling and SNV (Single Nucleotide Variant) calling from previously aligned bisulfite-treated reads. The script includes multiple quality-control related features. to. Estimation of the bisulfite conversion rate (MethylExtractBSCR_version.pl) The script calculates the bisulfite conversion rate from an unmethylated genome. In the case of plants, the script can be run with the reads aligned to the chloroplast genome, while in other organisms an unmethylated genome (as the phage lambda) must be added to the experimental setup. Statistical assessment of the bisulfite conversion rate(MethylExtractBSPvalue_version.pl) The script calculates the error probability (p-value) for each position using the binomial distribution, given an error interval for the methylation levels. In addition, the Benjamini-Hochberg step-up procedure has been implemented to control the false discovery rate. Note that the bisulfite conversion rate must be known to run this script.

Please be aware that this code is not being actively developed, as it is an archive of the code as it was at the time of publication in the associated F1000Research article. For the latest version of this code, please see http://bioinfo2.ugr.es/MethylExtract/.