SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
orthology search-Biomart or RBH bioman1 Bioinformatics 11 09-03-2012 11:22 AM
PubMed: Not all sequence tags are created equal: designing and validating sequence id Newsbot! Literature Watch 0 08-19-2012 12:51 AM
NGS whole genome sequence versus sequence capture for quality control houkto Bioinformatics 0 02-02-2012 05:16 AM
ensembl biomart 3' UTR problem NicoBxl Bioinformatics 0 04-07-2011 01:03 AM
In Sequence: Yale Team Uses an Illumina GA to Sequence Yeast Transcriptome; Finds Gre Newsbot! Illumina/Solexa 0 05-06-2008 03:02 PM

Reply
 
Thread Tools
Old 10-01-2012, 02:25 PM   #1
omiguele
Junior Member
 
Location: Mexico City

Join Date: Sep 2012
Posts: 7
Default Get upstream sequence with biomaRt

Hi Im trying to get 100bp upstream of some genes from a.gambiae. Im using biomaRt and my query looks like this:
vector<-useMart("vectorbase_mart_13",dataset="agambiae_eg_gene")

agambiaeseq<-getBM(attributes=c('start_position','end_position','chromosome_name','strand','ensembl_gene_id','gene_flank','upstream_flank'),filters='ensembl_gene_id',value='AGAP004677', mart=vector)


I know that for the attrbute 'upstream_flank' I should put the value 100 but I just dont know where.

Thank you for your attention

Last edited by omiguele; 10-01-2012 at 02:37 PM.
omiguele is offline   Reply With Quote
Reply

Tags
bioconductor, biomart, upstream_flank, vectorbase

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:41 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO