Hi Rohan,

You can relate the counts for 3UTR regions to gene IDs through the 
transcript IDs.

     txdb_file <- system.file("extdata", "UCSC_knownGene_sample.sqlite", 
package="GenomicFeatures")
     txdb <- loadFeatures(txdb_file)
     utr=threeUTRsByTranscript(txdb,use.names=FALSE)


The transcript names can be matched to the gene ID's through,

     txBygene <- transcriptsBy(txdb, "gene")
     geneID <- rep(names(txBygene), elementLengths(txBygene))
     df <- data.frame(geneID=geneID, 
txID=values(unlist(txBygene))[["tx_id"]])

Now you know what gene ID each tx count belongs to. You can split your 
counts by gene ID ...


Valerie



On 09/20/2011 12:13 PM, rohan bareja wrote:
> Hi everyone,
> I am doing NGS analysis using bam files.I have counted reads in 3'utr region using 
> utr=threeUTRsByTranscript(txdb,use.names=FALSE)
> countsUTR<- countOverlaps(utr,reads)
> I have got the transcript level counts from this.How can I get the gene level counts??It might sound silly but Does anybody have an idea on what type of anaylses we can do from this countsUTR ?
> Thanks,Rohan
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