Entering edit mode
5.4 years ago
Anu
•
0
I want to map methylation pattern (CpG sites) with the translocation breakpoints of the BRCA1 gene. From where I should start? what kind of software i should use to do the mapping?
It is unclear which data you have. What do you mean with
map methylation pattern?DNA methylation can induce genomic instability. It is also known that most hypermethylated genes are found in the regions of high-frequency chromosomal breakpoints across the human genome. Therefore, i am trying to map CpG sites( Methylated regions) and the translocation breakpoints in the Human Cancer Genome using bioinformatics tools.
What is of interest is the format of data you have. A BED file with the scores, fastq files, BAM files, bigwigs? That will decide what tool to be used (to be used first).
I don't have my own data. I want to use any methylation database and mutation data database available. I already have the access to the mutation database and i wanted to download some methylation data form a methylation database. Any suggestions?
I don't have my own data. I want to use any methylation database and mutation data database available. I already have the access to the mutation database and i wanted to download some methylation data form a methylation database. Any suggestions?
Shouldn't you have individuals of which you have both mutations and methylation before you can draw conclusions
If we consider one gene like BRCA1, we have the mutation data as well as the methylation data. By "mutation data" ,I meant a specific nucleotide sequence in the gene ( ex: repeat sequence or let's say a CpG island). I want to see how often they all overlap at specific translocation breakpoints ( which are also available in databases) in the gene. But this seems a complicated process.
Oh, so not actual mutation data. Sure, then you need a bed file of these features and then you can use BEDOPS or bedtools to look or overlaps.
well, i haven't used BEDOPS before but I'll try. Will it be an issue if we have thousands of genes? Do we need to do one by one?
Oh no that doesn't really matter. Looking for overlaps between intervals scales pretty well for sorted files.
Thank you. I will try it!