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Fenton Christopher Graham
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90
@fenton-christopher-graham-5504
Last seen 4.9 years ago
Illumina mapping nuId to genome coordinates.
>m2<- read.table("processed_data.csv", header=T, row.names=1,
sep="\t")
>probes<- rownames(m2)
>dd<- probeID2nuID(probes)
>seqs<- id2seq(dd[,7])
>test<- cbind(dd, seqs)
> test[grep("r33p5EJWUK57ZWL3no", test[,7]),]
Search_Key "XM_940724.1"
ILMN_Gene "A3GALT2"
Accession "NM_001080438.1"
Symbol "A3GALT2"
Probe_Id "ILMN_1668111"
Array_Address_Id "0001740066"
nuID "r33p5EJWUK57ZWL3no"
seq
"TCTTCTGGCTGCACAAGCCCGCCAAGGTGCTGTCGCCCGAGTTCTGCTGG"
Now if I BLAT the sequence against GRCh37/hg I get the following.
QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END
SPAN
YourSeq 50 1 50 50 100.0% 1 - 33772451 33772500
50
Unfortunately this is not near the CDS.
If I search UCSC for A3GALT2 I get the following location
chr1:33,772,365-33,778,183
Why are the chromosomal locations for this probe different?
Chris