Entering edit mode
18 months ago
godth13teen ▴ 70
Hi, I'm getting myself familiar with some microarray data analysis. I'm trying to follow the Infinium Controls training guide from illumina, but my working computer is not Windows (I'm using Linux), so is there any way that I can generate the QC report (staining, extension, target removal, hybridization, stringency, non-specific binding, non-polymorphic, restoration) without using Genome Studio? I think that they are intensities after all, and can be generated by some way. I can generate gtc any other downstream files from idat without Genome Studio.
Thank you very much
See if these past threads helpL
Are there any GenomeStudio alternatives to process Illumina genotyping array?
How can I create an Illumina report in Linux using IDAT files?
Or this package https://github.com/freeseek/gtc2vcf
Thanks for your answer.
Yes, I know how to generate GTC from IDAT files, but I'm asking about the QC report to run my pipeline entirely on command line.