[BioC] boiomaRt 'getSequence' question

[Steffen Durinck]

Hi Galina,

With biomaRt you can currently only specify either an upstream or downstream flank in one query.  So you'll need at least two queries to do this.  If you do ?getSequence, the help page will tell you that seqType "gene_exon_intron' gives the exons + introns of a gene.  Note that if you retrieve seqType gene_exon_intron, you are already retrieving the 5' and 3' UTRs flanking the coding region.  If you also want to include the promotor region in this query you could set upstream=4000.  If you need sequences downstream the transcribed region, you'll have to do a second query and match up both query results.

Cheers,
Steffen

----- Original Message -----
From: "Glazko, Galina" <Galina_Glazko at urmc.rochester.edu>
Date: Thursday, February 7, 2008 12:48 pm
Subject: [BioC] boiomaRt 'getSequence' question
To: bioconductor at stat.math.ethz.ch

> Dear all,
> 
> 
> 
> I have a list of ensemble gene IDs and I need to get corresponding
> sequences together with 5' upstream (4000 bp), 3'downstream (4000 bp)
> and all introns.
> 
> I know that I probably can do this using a combination of commands:
> 
> 
> 
> Tmp1<-getSequence(id=
> "ENSG00000128714",type="ensembl_gene_id",seqType="coding_gene_flank",ups
> tream=4000,mart=human)
> 
> Tmp2<-getSequence(id=
> "ENSG00000128714",type="ensembl_gene_id",seqType="coding_gene_flank",dow
> nstream=4000,mart=human)
> 
> Tmp3<- getSequence(id=
> "ENSG00000128714",type="ensembl_gene_id",seqType="cdna", mart=human)
> 
> 
> 
> and then concatenate tmp1, tmp2, tmp3, but I am not sure that 'cdna'
> seqType will give me introns...
> 
> Also, I hope that there is a simpler way to get all these sequences
> using just one command with the right 'seqType' specification.
> 
> 
> 
> Could someone please clarify this for me?
> 
> Thank you!
> 
> 
> 
> Best regards
> 
> Galina
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor