Question: how to obtain the locations of a exon and its corresponding peptide from a specific transcript in bioMart
gravatar for jjaeyun
4.6 years ago by
United States
jjaeyun0 wrote:

I tried to connect a transcript (ENSTxxx)'s exons to their corresponding peptides (residues) using bioMart in R.

ensembl<-  useMart("ensembl")
ensembl<- useDataset( "ensembl", dataset="hsapiens_gene_ensembl")
getBM(c('peptide_location','exon_chrom_start','exon_chrom_end'), filters = c('ensembl_transcript_id','pdb'), values=list('ENST00000606293','2ZA5'), mart=ensembl)
Error in getBM(c("peptide_location", "exon_chrom_start", "exon_chrom_end"),  : 
  Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed

I wish to get some help for this problem.
peptide exon biomart • 2.1k views
ADD COMMENTlink modified 4.6 years ago by informatics bot610 • written 4.6 years ago by jjaeyun0
gravatar for informatics bot
4.6 years ago by
United States
informatics bot610 wrote:

This has to do with the way the Biomart webserver/database is set up. Essentially, you can't do gene-based queries and transcript-based queries at one time. But you can do them sequentially and merge at the end.

transcript_data<-getBM(c('ensembl_transcript_id','exon_chrom_start','exon_chrom_end'), filters = c('ensembl_transcript_id','pdb'), values=list('ENST00000606293','2ZA5'), mart=ensembl)
pept_data<-getBM(c('ensembl_transcript_id','peptide_location'), filters = c('ensembl_transcript_id','pdb'), values=list('ENST00000606293','2ZA5'), mart=ensembl)
final_data<-merge(transcript_data, pept_data, by='ensembl_transcript_id')
ADD COMMENTlink modified 6 months ago by RamRS27k • written 4.6 years ago by informatics bot610

Thank you so much! It worked. And, it answers for my rest of work. Thanks again!

BTW, this was my first use of Biostart. This is pretty nice

ADD REPLYlink written 4.6 years ago by jjaeyun0

You're very welcome :D

feel free to up-vote my "answer" and mark this question as solved.

ADD REPLYlink written 4.6 years ago by informatics bot610

Hi Lando,

I thought your code was what I wanted, but actually, it is not.

In your merge function at the end, it was supposed to be exon range or exon id, other than transcript id. Could you correct this?


ADD REPLYlink modified 6 months ago by RamRS27k • written 4.6 years ago by jjaeyun0
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