Problems with mapping chromosomal probe locations for illumina probes ?!
1
0
Entering edit mode
@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
probe probe • 1.0k views
ADD COMMENT
0
Entering edit mode
@philippe-dessen-288
Last seen 10.2 years ago
Hello, The gene A3GALT2 has been renamed as a pseudogene see Entrez Gene A3GALT2 – alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase) [Homo sapiens] alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase) Official Symbol: A3GALT2 Chromosome: 1; Location: 1p35.1 This record was replaced with GeneID: 127550 When you blat the probe on UCSC you can see it is in the 3'part (non coding !) of 2 enSembl transcripts A3GALT2P at chr1:33772367-33777822 - (ENST00000330379) A3GALT2P at chr1:33772367-33778491 - (ENST00000442999) Best Philippe Le 15 janv. 2013 à 13:30, Fenton Christopher Graham a écrit : > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENT

Login before adding your answer.

Traffic: 471 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6