Hi,
I have been checking some gene predictions and for this reason I aligned
the tables
"knownGene" WITH "kgXref" from track: UCSC Genes, group: Genes and
Gene Prediction Tracks, assembly: Mar.2006
This alignment deleted (excluded) all chrom13 entries from "knownGene".
"kgXref" has not got a chromosome entry, but it looks as if the file has
all entries referring to chr13 missing. See R snippet:
knowngenes<-read.table(paste(d.dir,"knownGene_hg18_full.tabular",sep=""),sep="\t",header=F)
names(knowngenes)<-c("name", "chrom","strand","txStart","txEnd",
"cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds",
"proteinID", "alignID")
kgXref<-read.table(paste(d.dir,"kgXref.tabular",sep=""),sep="\t",header=F)
names(kgXref)<-c("name","mRNA","spID","spDisplayID", "geneSymbol",
"refseq", "protAcc", "description")
knowngenes_ref<-merge(knowngenes,kgXref,by="name", all.x=T)
knowngenes_ref[knowngenes_ref$chrom=="chr13",]
See below. Could you help with that?
Many thanks,
Beate
57554 NP_001121164 uc010aga.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57555 O95965 uc010agb.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57556 Q86UB2-2 uc010agc.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57557 uc010agd.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57558 uc010age.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57559 P49917 uc010agf.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57560 A8K8Q4 uc010agg.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57561 P49917 uc010agh.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57562 Q7L211 uc010agi.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57563 Q7Z5J2 uc010agj.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57564 A6H8Y0 uc010agk.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57565 uc010agl.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57566 Q9UK53-3 uc010agm.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57567 NP_003890 uc010agn.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
57568 uc010ago.1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
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