Entering edit mode
3.2 years ago
avichaireich
▴
10
Hello.
Is there a way to retrieve a list of snps from Affymetirx microarray files, such as cychp, CEL, cdf file etc? I know how to retrieve a snp list from these files when they are loaded to the Chromosome Analysis Suite (ChAS) software, but the software can export the snp list one file at a time, while I'm looking for a way to retrieve snp list from multiple Affymetirx microarray files.
I'm referring to CytoScan750k_array files.
Thank you.
How many samples have you? The CytoScan was not as popular as Affymetrix had hoped; so, there is not much support for it. Does Genotyping Console not support it? (note that Genotyping Console is no longer supported, either).
I have hundreds of samples and I'm trying to write a script that will run on all the samples and extract from them their snp list. In addition, I'm working in Unix platform so a software for Windows will not help me. Is their a R package or a command-line tool that can extract the snp list?
Take a look at the 'aroma affymetrix' project. Otherwise, I can only suggest that you perform further searching. I am not aware of anything.