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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>
>
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