Hi Hervé

    Thank you for the detailed instructions!  They do help.

Best,
ZQ


On Fri, Jan 3, 2014 at 6:33 AM, Hervé Pagès <hpages@fhcrc.org> wrote:

> Hi ZQ,
>
>
> On 01/01/2014 12:51 AM, Zhi-Qiang Ye wrote:
>
>> Hi, thanks for your help.
>>
>> The information I need is the 'rn4' coordinates of Entrez Genes,  so I
>> finally used the 'refGene' table and 'refLink' table downloaded from UCSC
>> genome browser database under the directory of 'rn4', and got what I need.
>>
>
> Following Steve's original suggestion (but using the refGene table
> instead of ensGene):
>
>   library(GenomicFeatures)
>   txdb <- makeTranscriptDbFromUCSC(genome='rn4', tablename='refGene')
>   gn <- genes(txdb)
>
> This gives you the 'rn4' coordinates of Entrez Genes:
>
>   > head(gn)
>   GRanges with 6 ranges and 1 metadata column:
>               seqnames                 ranges strand |         gene_id
>                  <Rle>              <IRanges>  <Rle> | <CharacterList>
>     100034253     chrX [ 40301219,  40334396]      - |       100034253
>     100036582     chr8 [ 18755584,  18756808]      + |       100036582
>     100036765    chr12 [ 32898194,  32924599]      + |       100036765
>     100049583     chr8 [114071508, 114072510]      - |       100049583
>     100124593     chr8 [128569564, 128570618]      + |       100124593
>     100125361    chr10 [ 45764849,  45775258]      - |       100125361
>     ---
>     seqlengths:
>              chr1         chr2         chr3 ...        chrUn chrUn_random
>         267910886    258207540    171063335 ...     75822765      6862066
>
>   > head(as.character(mcols(gn)$gene_id))
>   [1] "100034253" "100036582" "100036765" "100049583" "100124593"
> "100125361"
>
> Note that makeTranscriptDbFromUCSC() downloads and uses the 'refGene'
> and 'refLink' tables from UCSC for you in order to generate the
> TranscriptDb object 'txdb'. In addition to being convenient, this
> method also avoids some of the common pitfalls of downloading and
> processing those tables "manually".
>
> Cheers,
> H.
>
>
>  As for other information not related to the chromosomal locations, I just
>> used the information in the package  'org.Rn.eg.db'.
>>
>> Maybe the maintainner can still provide official packages based on 'rn4',
>> say, 'org.Rn4.eg.db', since annotation based on 'rn5' is not as complete
>> as
>> that based on 'rn4'.
>>
>> Best,
>> ZQ
>>
>> On Sat, Dec 21, 2013 at 8:53 AM, Marc Carlson <mcarlson@fhcrc.org> wrote:
>>
>>  Steve is right.  You could go and do that.  However in this case we have
>>> already done the work for you.  You can find a package here:
>>>
>>> http://www.bioconductor.org/packages/release/data/annotation/html/TxDb.
>>> Rnorvegicus.UCSC.rn4.ensGene.html
>>>
>>> That should get you transcript locations for RN4.
>>>
>>> For more information about how you can make use of that resource and of
>>> others like it, please be sure to also peak at our workflow:
>>>
>>> http://www.bioconductor.org/help/workflows/annotation/annotation/
>>>
>>>
>>>    Marc
>>>
>>>
>>>
>>>
>>>
>>> On 12/18/2013 10:09 PM, Steve Lianoglou wrote:
>>>
>>>  Hi,
>>>>
>>>> On Wed, Dec 18, 2013 at 6:20 PM, Zhi-Qiang Ye <yezhiqiang@gmail.com>
>>>> wrote:
>>>>
>>>>  Hi, all
>>>>>
>>>>>           I need to analysis genes whose chromosomal locations are
>>>>> based
>>>>> on
>>>>> the rat genome version rn4, so installed 'org.Rn.eg.db'. However, the
>>>>> genome coordinate system is based on rn5.
>>>>>
>>>>>            Is there any way to get and install old versions of
>>>>> 'org.Rn.eg.db'?
>>>>>
>>>>>  You might consider building a TranscriptDb object from rn4 annotations
>>>> using the GenomicFeatures package:
>>>>
>>>> http://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html
>>>>
>>>> Read through its vignette to figure out how to download and build a
>>>> TranscriptDb from UCSC. It's going to be something like:
>>>>
>>>> R> library(GenomicFeatures)
>>>> R> txdb <- makeTranscriptDbFromUCSC(genome='rn4', tablename='ensGene')
>>>>
>>>> Keep reading to figure out how to lookup genes/transcripts by
>>>> (ensembl) transcript IDs, and I think you should be good to go.
>>>>
>>>> If you need to do sequence related analyses using these annotations,
>>>> you can use the rn4 BSgenome object, to boot:
>>>>
>>>> http://bioconductor.org/packages/release/data/annotation/html/BSgenome.
>>>> Rnorvegicus.UCSC.rn4.html
>>>>
>>>> HTH,
>>>> -steve
>>>>
>>>>
>>>>  _______________________________________________
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>>>
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>>
>>
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>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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