Working examples

[How to cite NGSmethDB]

Retrieving and analyzing NGSmethDB data through UCSC track hubs and the Galaxy platform

We provide here some examples for retrieving NGSmethDB data from UCSC Table Browser and Data Integrator and analyzing them in the Galaxy platform. One of the ways in which NGSmethDB data are distributed to the community is through standard track hubs, which can be then uploaded into the main genome platforms, as UCSC (Kent et al., 2002) or ENSEMBL (Yates et al., 2016) genome browsers, where they can be easily browsed in the form of genome-wide methylation maps. In addition, numerical data in tabular form can be easily retrieved to the local computer through the standard tools built in these platforms (UCSC Table Browser or Data Integrator) or sent to other software platforms (Galaxy (Afgan et al., 2016), GREAT  (McLean et al., 2010) or GenomeSpace (Qu et al., 2016)) for downstream analyses. We describe below some working examples using these tools to retrieve NGSmethDB numerical data, as well some Galaxy workflows to carry out some simple tasks.

  1. Retrieve a list of methylation levels at single cytosines for a given tissue in a particular gene, genome region, chromosome or entire genome
  2. Retrieve a list of differentially methylated cytosines (DMCs) for a given tissue in a particular gene, genome region, chromosome or entire genome
  3. Compare the cytosine methylation levels in a set of tissue samples from the same or different individuals
  4. Average methylation in the genes from a given region

Note: For examples of retrieving NGSmethDB data using programmatic and HTTP access see the NGSmethDB Manual.

References

Afgan, E., Baker, D., van den Beek, M., Blankenberg, D., Bouvier, D., Čech, M., … Goecks, J. (2016). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research, gkw343. http://doi.org/10.1093/nar/gkw343

Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler,  a. D. (2002). The Human Genome Browser at UCSC. Genome Research, 12(6), 996–1006. http://doi.org/10.1101/gr.229102

McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., … Bejerano, G. (2010). GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnology, 28(5), 495–501. http://doi.org/10.1038/nbt.1630

Qu, K., Garamszegi, S., Wu, F., Thorvaldsdottir, H., Liefeld, T., Ocana, M., … Mesirov, J. P. (2016). Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nature Methods, 13(3), 245–247. http://doi.org/10.1038/nmeth.3732

Yates, A., Akanni, W., Amode, M. R., Barrell, D., Billis, K., Carvalho-Silva, D., … Flicek, P. (2016). Ensembl 2016. Nucleic Acids Research, 44(D1), D710–6. http://doi.org/10.1093/nar/gkv1157