i have the following problem. I need to compute and visualize cytosine methylation levels around splice junctions. I already used TopHat to determine splice junctions. Therefor i used RNA-Seq reads (obtained from spleen cell) downloaded at Roadmap Epigenomics Project and the hg19 as reference genome. I also found the methylation data obtained from the same spleen sample at this homepage. They are provided raw reads (SRR files) and as processed data in bed and wig format. I would prefer to extract the processed methylation data out of the bed/wig file instead of using the raw data, so i would like to know:
- Is there any good tool to extract the methylation data out of the bed/wig file and map it to the regions +200 nt and -200 nt left and right of the splice junctions previously computed with TopHat?
- Is there a good tool for visualization?
- Which tool can i use for statistical analysis? Maybe R Package(s)?
I hope someone can help me here :)