How To Remap Humanht V4 Chips To Hg19?

Question

[liu4gre]

I currently have the version mapped to hg18, and the head of the file is "TargetID ProbeID AVG_Signal BEAD_STDERR Avg_NBEADS Detection Pval". I wanna remap it to hg19 version so that I can compare it with other data. How should I do that? This probeID is the probeset id (e.g. 6450255 2570615)?

Answer 1

[Charles Warden]

The annotations may already be there, but I would first download the manifest file for your array (below is the corresponding link for the latest HumanHT array)

http://support.illumina.com/array/array_kits/humanht-12_v4_expression_beadchip_kit/downloads.ilmn

If you have a column with hg18 coordinates, you can extract that column and use a LiftOver tool (such as the one in Galaxy) to convert those to hg19 coordinates. In the latest version, these are in the Chromosome, Probe_Chr_Orientation, and and Probe_Coordinates columns (although I think the latest array is already mapped to hg19).

If you only have sequences from probes, you can locally BLAT or BLAST those probes against hg19. This will take longer, but it will work (and you can verify that you believe the mapping this way, if you only consider probes with unique mappings). In the latest version, this comes from the Probe_Sequence column.

[liu4gre]

Thanks. I have the coordinates. So I am gonna try liftover