Abrita Chakravarty

The "Methylation Viewer" is an application to view - "Active Regions" - which are methylated DNA sequences from a particular experimental dataset.

Run Methylation Viewer

Instructions:

1. First load the methylation data using Load -> Load Methylation Data. (Sample file Y.methylation provided here.)
2. Next, either load the respective sequences for the methylated regions or histone modification data.
   • To load sequences, use Load -> Load Sequence. (Sample file Y.sequence provided here.)
   • To load the histone modifications use Load -> Load Histone Modification. You may select an entire folder containing files for different histone modifications or select a particular histone modification file. (Samples provided here.)
3. The format for the names of the files and the data in them must be the same as shown in the samples. Data for only one chromosome may be loaded at a time.
4. Once all the data are loaded, it is possible to search for a particular "Active Region" using either its id, start or end co-ordinates or associated genes.
5. If a number is provided for the "Search for CGs with spacing" field, the search will highlight CG dinuceotide pairs with the given spacing between them.
6. If a particular histone modification is selected, the search will align the locations of the histone modifications along the sequence of the active region.