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Question: biomaRt: no access to Ensembl_75 (GRCh37.p13)
0
gravatar for Jennifer Becq
3.1 years ago by
Jennifer Becq0 wrote:

Hi,

biomaRt seems to only give access to Ensembl Genes 77 now (listMarts()) and the archive option (listMarts(archive=TRUE)) goes back too far in time (from Ensembl 47 and earlier). Is it possible to access Ensembl Genes 75 for those still using GRCh37 from biomaRt? 

Thank you!

Jenn

 

> listMarts()

                                 biomart
1                                ensembl
2                                    snp
...

                                                                                                 version
1                                                                            ENSEMBL GENES 77 (SANGER UK)
2                                                                        ENSEMBL VARIATION 77 (SANGER UK)
...


> listMarts(archive=TRUE)

                      biomart                     version
1              ensembl_mart_47   ENSEMBL GENES 47 (SANGER)
2     genomic_features_mart_47            Genomic Features

...

> sessionInfo()
R version 3.0.2 Patched (2013-10-27 r64116)
Platform: x86_64-unknown-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=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] biomaRt_2.22.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.24.0 Biobase_2.22.0       BiocGenerics_0.8.0  
 [4] DBI_0.3.1            IRanges_1.20.7       parallel_3.0.2      
 [7] RCurl_1.95-4.1       RSQLite_0.11.4       stats4_3.0.2        
[10] tools_3.0.2          XML_3.98-1.1        

 

 

ADD COMMENTlink modified 3.0 years ago by springbreeze.autumncolor0 • written 3.1 years ago by Jennifer Becq0
4
gravatar for Thomas Maurel
3.1 years ago by
Thomas Maurel700
United Kingdom
Thomas Maurel700 wrote:

Dear Jen,

We have created an Ensembl GRCh37 archive website accessible through the following URL: http://grch37.ensembl.org

You can access this archive through BiomaRt by setting up a different host in the useMart function:

grch37 = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="hsapiens_gene_ensembl")

Alternatively, you can set your host to connect to the ensembl mart 75 database located on our archive website (http://feb2014.archive.ensembl.org/index.html):

ensembl_75 = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="feb2014.archive.ensembl.org", path="/biomart/martservice", dataset="hsapiens_gene_ensembl")

Hope this helps,

Best Regards,

Thomas

 

ADD COMMENTlink written 3.1 years ago by Thomas Maurel700
0
gravatar for Jennifer Becq
3.1 years ago by
Jennifer Becq0 wrote:

It works perfectly, thank you!

Jennifer

ADD COMMENTlink written 3.1 years ago by Jennifer Becq0
0
gravatar for springbreeze.autumncolor
3.0 years ago by
United States

Sorry, I have another question related to it.

I'd like to retrieve GRCh37 sequence data using getSequence. 

However, getSequence doesn't work when I use the above marts (grch37=useMart(biomart="ENSEMBL_MART_ENSEMBL"..., or ensembl_75)

seqtemp     <- getSequence(id = "ENST00000334785", type="ensembl_transcript_id", mart =grch37, seqType = "transcript_exon_intron")

The error message is as follows.

Error in martCheck(mart, "ensembl") :
  This function only works when used with the ensembl BioMart.
Calls: findtranscript -> GetSeq -> getSequence -> martCheck

How can I solve it?

I'd be grateful if you could give me some suggestion or solution.

 

Thank you!

Kaoru

 

PS.

Actually, I tired to use two kinds of mart like

  mart = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host=marthostname)
  seqmart = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="feb2014.archive.ensembl.org", path="/biomart/martservice", dataset="hsapiens_gene_ensembl")

I employed mart when I retrieved GRCh37 gene annotation and I employed seqmart when I retrieve sequence data.

But, I sometimes found inconsistency between GRCh37 annotation and GRCh38 sequence

e.g. in ENST00000359842, the transcript_exon_intron length is 44275 bp in GRCh37 (caluculated by start end position retrieved by getBM) , while it is 44280 bp in GRCh38  (calculated from actual sequence length retrieved by getSequence)

When I employed GRCh37 ensembl for getBM and getSequence, this never happened.

 

 

 

 

 

 

 

 

ADD COMMENTlink written 3.0 years ago by springbreeze.autumncolor0
0
gravatar for Steffen Durinck
3.0 years ago by
Steffen Durinck90 wrote:

Hi Kaoru,

I fixed this in the dev version of biomaRt (2.23.1)  now you should be able to use getSequence on biomart ENSEMBL_MART_ENSEMBL

Cheers,

Steffen

 

ADD COMMENTlink written 3.0 years ago by Steffen Durinck90
0
gravatar for springbreeze.autumncolor
3.0 years ago by
United States

Hi Steffen,

I downloaded biomaRt 2.23.1 and I found my script ran correctly.

You are my lifesaver!

 

Thousand thanks,

Kaoru

 

 

 

 

ADD COMMENTlink written 3.0 years ago by springbreeze.autumncolor0
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