Question: Are there any GenomeStudio alternatives to process Illumina genotyping array?
2
gravatar for Zhenyu Zhang
7 weeks ago by
Zhenyu Zhang260
United States
Zhenyu Zhang260 wrote:

The mouse clicking interface of GenomeStudio is so unfriendly for large and continuous data production. - Do we have alternatives to this that can process Illumina genotyping array idat files? - Or do you have any suggestions to automate the GenomeStudio process with command lines? Thanks

ADD COMMENTlink modified 9 days ago by steffanchristiansen0 • written 7 weeks ago by Zhenyu Zhang260

I am basically in the same spot. I just started looking at genomestudio today, so I have not dug very deep yet. I'm sure they worked really hard on this, but a windows only GUI bioinformatics tool is a bit odd. Did you end up coming across any alternatives?

ADD REPLYlink written 28 days ago by brett.vanderwerff130

It seems some basics can be done with GS command lines, but still in windows.

ADD REPLYlink written 27 days ago by Zhenyu Zhang260
0
gravatar for steffanchristiansen
9 days ago by
University of Copenhagen
steffanchristiansen0 wrote:

The crlmm package in R should be able to do it. However, in my own experience it is difficult to run it for Omni5 generated data. I guess it depends on which genotype array you are using. Alternatively, beadarray should also be able to read idat files but I have not tried that package yet.

ADD COMMENTlink written 9 days ago by steffanchristiansen0
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