[BioC] TXNAME mapping

[Murli [guest]]

Hi, 

I am annotating my reads using TxDb.Hsapiens.UCSC.hg19.knownGene and org.Hs.eg.db. I am able to get everything work and also merge the data, but when I reviewd the output I see that the same TXNAME is mapped to different locations. See part of the output below. TXNAME uc003ytw.3 is associated with chr8  13515402  13515702   301 and  chr12  71612488  71612788   301.  I thought it should be unique, I would appreciate if you could correct me if I am missing something in understanding TXNAME. 

Thanks ../Murli



 
>mrg.data[1000:1100,]
      TXID GENEID     TXNAME seqnames     start       end width strand
1000 32071   7038 uc003ytw.3     chr8  13515402  13515702   301      *
1001 68728  63934 uc002qnd.3     chr8  14339379  14339679   301      *
1002 68729  63934 uc002qne.3     chr8  14339379  14339679   301      *
1003 68730  63934 uc010etm.3     chr8  14339379  14339679   301      *
1004 32071   7038 uc003ytw.3     chr8  14339379  14339679   301      *
1005 68728  63934 uc002qnd.3    chr12  71612488  71612788   301      *
1006 68729  63934 uc002qne.3    chr12  71612488  71612788   301      *
1007 68730  63934 uc010etm.3    chr12  71612488  71612788   301      *
1008 32071   7038 uc003ytw.3    chr12  71612488  71612788   301      *
1009 68728  63934 uc002qnd.3    chr14  24809972  24810272   301      *
1010 68729  63934 uc002qne.3    chr14  24809972  24810272   301      *




 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] Homo.sapiens_1.1.1                     
 [2] GO.db_2.9.0                            
 [3] OrganismDbi_1.2.0                      
 [4] org.Hs.eg.db_2.9.0                     
 [5] RSQLite_0.11.4                         
 [6] DBI_0.2-7                              
 [7] VariantAnnotation_1.6.6                
 [8] Rsamtools_1.12.3                       
 [9] BSgenome.Hsapiens.UCSC.hg19_1.3.19     
[10] BSgenome_1.28.0                        
[11] Biostrings_2.28.0                      
[12] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2
[13] GenomicFeatures_1.12.2                 
[14] AnnotationDbi_1.22.6                   
[15] Biobase_2.20.0                         
[16] GenomicRanges_1.12.4                   
[17] IRanges_1.18.1                         
[18] BiocGenerics_0.6.0                     

loaded via a namespace (and not attached):
 [1] biomaRt_2.16.0     bitops_1.0-5       graph_1.38.2       RBGL_1.36.2       
 [5] RCurl_1.95-4.1     rtracklayer_1.20.2 stats4_3.0.1       tools_3.0.1       
 [9] XML_3.98-1.1       zlibbioc_1.6.0 

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