Illumina cpg probe ID conversion to chromosomal location?

Question

[ahsan.raza.rana]

from where to get mouse 450K cpgmethylation annotation file Please guide me if any one having information related to this and what are gold standards for annotatiopn

I want to get list of all the CpG probes of Illumina 27K or 450K whatever is available.Then I want to get the chromosome number, genomic position that each probe represents.. I am doing for mouse genome . Can any one help me how to do it? Can I use some data base to download CpG probe list of mouse or some package?

[mbk0asis]

I'm not sure if they have mouse data, but for human, you can download from this link below.

http://support.illumina.com/array/array_kits/infinium_humanmethylation450_beadchip_kit.html

Click 'Infinium HumanMethylation450K v1.2 Product Files', then you will see the manifest file in csv format.

[Kermit]

nice. this manifest contains CHR, COORD, SNP, and even some gene symbol annotations

[ahsan.raza.rana]

thanks but there I am not finding manifest file in .csv format. there is only .opa format of manifest file and that is for mouse snp. could u plz be kind enough to check that

[ahsan.raza.rana]

from where to get mouse 450K cpgmethylation annotation file Please guide me if any one having information related to this and what are gold standards for annotatiopn

[mastal511]

I don't think they do a mouse array. This Illumina page http://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html has manifest files (in csv and bpm format) for the human array, and an excel file with the explanation of the column headers for the manifest file.

[jack]

Dear Mastal511, do you know how we can download these files? They are not available for download. "This system is for the use of authorized users only. " Thank you.

[ahsan.raza.rana]

so,from where can i get such type of info for mouse methyalted cpg.Can I use the cpgislands list from UCSC as probes for this purpose and can calculate such information by using some functions available in R package.

[ahsan.raza.rana]

I dont know wether they have any mouse array or not? Does any one know?

[jotan]

Google says no. Did you not check before posting?

Answer 1

[ahsan.raza.rana]

so,from where can i get such type of info for mouse methyalted cpg.Can I use the cpgislands list from UCSC as probes for this purpose and can calculate such information by using some functions available in R package.

[jotan]

Does Illumina have a mouse array?