MethylPy pipeline

[amshahri]

My goal was to submit an analysis pipeline for 3% grade increase, but unfortunately, I was not able to run it due to some technical issues,

methylpy is an analysis cellular pipeline to get the DNA methylation data. DNA methylation is a process in which methyl groups are attached to the DNA molecules(Robertson, 2018).

methylpy :
1- First we need to load the data, which is a bisulfite sequence that is being used for methylation analysis (BS-Seq)
2-building the reference data with a built-in function of methylpy
3-Processing the data (In which the methylation score or level of each cytosine would be measured)
4-Find the differentially methylated regions or DMRs
5-Converting the DMRs to filetypes of .bed & .bw in order to visualize it in a program like IGV
(all these steps are taken from the methylpy GitHub page (Schultz et al., 2015)

I found this pipeline on a paper in Nature with the title of: "Unique cell-type-specific patterns of DNA methylation in the root meristem" https://www.nature.com/articles/nplants201658
Due to some difficulties with Ubuntu on my personal computer I was not able to download some tools that are needed for methylpy, I even tried to work with it on the DataHub even though I uploaded the data on there which was over 10 GB, but due to some unknown reasons I started getting errors while installing some new needed tools for methylpy

Nature Paper :
Kawakatsu, T., Stuart, T., Valdes, M., Breakfield, N., Schmitz, R. J., Nery, J. R., . . . Ecker, J. R. (2016). Unique cell-type-specific patterns of DNA methylation in the root meristem. Nature Plants, 2(5), 16058. doi:10.1038/nplants.2016.58

mehtylpy Github:
Matthew D. Schultz, Yupeng He, John W.Whitaker, Manoj Hariharan, Eran A. Mukamel, Danny Leung, Nisha Rajagopal, Joseph R. Nery, Mark A. Urich, Huaming Chen, Shin Lin, Yiing Lin, Bing Ren, Terrence J. Sejnowski, Wei Wang, Joseph R. Ecker. Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation. Nature. 523(7559):212-216, 2015 Jul.

Robertson, S. (2018). Retrieved from https://www.news-medical.net/life-sciences/What-is-DNA-Methylation.aspx