Entering edit mode
4.1 years ago
MOJ
•
0
Can I annotate Illumina's Microarray manifest of file (GSA)? I tried with following steps: 1. Download Clinvar FTP from UCSC 2. Parse GSA file with the downloaded file. Kindly, let me know the feedback on the same
I have also tried with SNPnexus. But could not since SNPnexus accepts only 100,000 SNPs in one go and takes hell tot of time.
Hello, can you please describe the data that you currently have, and what you want to add to it? It seems that you want to add ClinVar variant information to your Illumina annotation?
I have .bpm file. The file contains following heading.
It is manifest file used to analyse microarray data with GenomeStudio. The file has all the information except rsid annotation with disease/condition. Hence, want to do the same.
You could try to annotate these within R by using biomaRt, with an example being here:
You will have to develop my code to suit your own situation, though.