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?
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ahsan.raza.rana •
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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.
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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.
nice. this manifest contains CHR, COORD, SNP, and even some gene symbol annotations
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
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 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.
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.
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.
I dont know wether they have any mouse array or not? Does any one know?
Google says no. Did you not check before posting?