Hi
Can someone please help with this issue.
How can I download methylation array raw files containing mutation in gene A from GDC legacy archive ?
Any help is vary much appreciated .
Sincerely
The TCGA methylation data is available as open access Beta (β) values from the Illumina Infinium 27K and 450K Human Methylation arrays. You can download all of this data from the GDC Legacy Archive. Here, I have configured a listing for ovarian cancer (TCGA-OV):
Note the different platforms under the Platform tab.
The open access mutation data I available as MAF (mutation annotation format) files. Again, there is data from different platforms. Here, I have configured this for you for the Illumina HiSeq:
To download the data, download the sample manifest for each listing and then use the GDC Data Transfer Tool. Once you get all of the data, you can then begin to think about a strategy of aligning them in order to find mutations overlapping methylated regions.
The study that you want to conduct is essentially methylation-quantitative trait loci (meQTL), I believe. I recommend that you look up previous literature not the subject once you have obtained all of your data, such as Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue.
Good luck
Kevin
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version 2.3.6
Thanks I was able to compare TCGA id from GDC data portal and in GDC archive to recognize samples containing mutations.