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[Bioc-devel] Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency

Martin Morgan
On 06/08/2015 11:43 PM, Rainer Johannes wrote:
Two other sources of Ensembl TxDb's are GenomicFeatures::makeTxDbFromBiomart() 
and AnnotationHub. For the latter, I'll add a variant of the following to the 
AnnotationHub HOWTO vignette 
http://bioconductor.org/packages/devel/bioc/html/AnnotationHub.html later today.

## Gene models

_Bioconductor_ represents gene models using 'transcript'
databases. These are available via packages such as
[TxDb.Hsapiens.UCSC.hg38.knownGene](http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.knownGene.html),
or can be constructed using functions such as
`[GenomicFeatures](http://bioconductor.org/packages/GenomicFeatures.html)::makeTxDbFromBiomart()` 
or `GenomicFeatures::makeTxDbFromGRanges()`.

_AnnotationHub_ provides an easy way to work with gene models
published by Ensembl. Here we discover the Ensemble release 80 r
esources for pufferfish,_Takifugu rubripes_

```{r takifugu-gene-models}
query(ah, c("Takifugu", "release-80"))
```

We see that there is a GTF file, as well as various DNA
sequences. Let's retrieve the GTF and top-level sequence files. The
GTF file is imported as a _GRanges_ instance, the DNA sequence as a
compressed, indexed Fasta file


```{r takifugi-data}
gtf <- ah[["AH47101"]]
dna <- ah[["AH47477"]]

head(gtf, 3)
dna
head(seqlevels(dna))
```

It is trivial to make a TxDb instance

```{r takifugi-txdb}
library(GenomicFeatures)
txdb <- makeTxDbFromGRanges(gtf)
````

and to use that in conjunction with the DNA sequence, e.g., to find
exon sequences of all annotated genes.

```{r takifugi-exons}
library(Rsamtools)     # for getSeq,FaFile-method
exons <- exons(txdb)
getSeq(dna, exons)
```

Some difficulties arise when working with this partly assembled genome
that require more advanced GenomicRanges skills, see the
[GenomicRanges](http://bioconductor.org/packages/GenomicRanges.html)
vignettes, especially "GenomicRanges HOWTOs" and "An Introduction to
GenomicRanges".
If instead of "genes" you do "transcripts", you will see 20 different
-Robert
http://www.ncbi.nlm.nih.gov/gene/672

  
    

      
      
    

  


  


  


  
  

    

  

    
      
    
    
Thread (9 messages)

  

  

    
            
        Ludwig Geistlinger
        
        Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
      
      Jun 3
    
    
      
            
        Robert M. Flight
        
        Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
      
      Jun 3
    
    
      
            
        Rainer Johannes
        
        Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
      
      Jun 8
    
    
      
            
        Ludwig Geistlinger
        
        Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
      
      Jun 9
    
    
      
            
        Rainer Johannes
        
        Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
      
      Jun 9
    
    
      
            
        Martin Morgan
        
        Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
      
      Jun 9
    
    
      
            
        Ludwig Geistlinger
        
        Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
      
      Jun 10
    
    
      
            
        Rainer Johannes
        
        Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
      
      Jun 10
    
    
      
            
        Rainer Johannes
        
        Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency
      
      Jun 11