SssICalc Source Code

This is our model of MBD pulldown alignments generated from SssI-treated DNA proposed in the publication entitled "A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction". Please read through the instructions in the README before using the software. Test files are provided in the "source" folder. Links to the indexes of CpGs in hg18 and the corresponding y_{i Λ} file, generated from that list using our experimental presets and summed on 10bp windows, are also given.

• README.md
• source.tar.gz (260MB)
• hg18_cpgs.txt.gz (82MB)
• hg18_Lambdas_10bp_MorelandEtal.txt.gz (2.3G)

An additional set of example scripts to aid in analysis:

• Generate a list of all CpG locations on hg19 using R: write_table_CpGs.R
• Convenient version of SssICalc when read length distribution is just described by mean: source_avg_l.tar.gz (136MB)
• Add calculated SssI values to BayMethList object (from Repitools package)for analysis: calcSssI_with_BayMethList.R with data (calcSssI_with_BayMethList_data.RData)