Question: Illumina cpg probe ID conversion to chromosomal location?
1
gravatar for ahsan.raza.rana
4.1 years ago by
ahsan.raza.rana40 wrote:

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?

chip-seq • 7.1k views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by ahsan.raza.rana40

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.

ADD REPLYlink written 4.1 years ago by mbk0asis530

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

ADD REPLYlink written 4.1 years ago by ahsan.raza.rana40

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

ADD REPLYlink written 4.1 years ago by ahsan.raza.rana40
1

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.

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by mastal5112.0k

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.

ADD REPLYlink written 2.1 years ago by jack0

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.

ADD REPLYlink written 4.1 years ago by ahsan.raza.rana40

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

ADD REPLYlink written 4.1 years ago by ahsan.raza.rana40

Google says no. Did you not check before posting?

ADD REPLYlink written 4.1 years ago by jotan1.2k
0
gravatar for ahsan.raza.rana
4.1 years ago by
ahsan.raza.rana40 wrote:

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.

ADD COMMENTlink written 4.1 years ago by ahsan.raza.rana40

Does Illumina have a mouse array?

ADD REPLYlink written 4.1 years ago by jotan1.2k
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