Query by helene_thygesen: Affy SNP-chip metadata – how to go through the probe sequences?
I have Affymetrix SNP-chip (250 K genomic) information. For each and every gene there are 56 probes =7 “quartets” (windows)*AB*PMMM*SenseAS. The data in the accompagnying CDF/TXT file appears like
SNP_A-1780520 rs16994928 ggatagtgttgacctc[A/G]agtacaggtttcaaaa 496 // 47873735 // 47874230 . .eleven .
ProbeSetID Chromosome Expr1002 PhysicalPosition AlleleA dbSNPRSID
SNP_A-1780520 twenty 47874178 47874178 A rs16994928
I require to intepret these meta-information in phrases of the probe sequences. In particular, in which in the ggatagtgttgacctc[A/G]agtacaggtttcaaaa string are the seven quartets and how does the MM probe difer from PM probe
Answer by Iain N
You can find assist right here
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