Question: How to annotate positions using biomaRt R package?
0
gravatar for abc
3.1 years ago by
abc30
abc30 wrote:

I have some genome positions and I want to annotate these positions (find Ensembl gene ID, the features like exonic, intronic, ...) using biomaRt R package.

part of my data

chr start stop strand
chr10 100572320 100572373 - 
chr10 100572649 100572658 +
bioinformatics biomart R • 1.2k views
ADD COMMENTlink modified 6 months ago by RamRS20k • written 3.1 years ago by abc30

What do these regions represent?  Doing what you suggest with biomaRt is possible, but it is going to be very tedious.  Perhaps there is another tool that is a better fit, but we need to know a little more detail before suggesting.

ADD REPLYlink written 3.1 years ago by Sean Davis25k

There Polyadenylation sites and I want to know if they are intronic (annotate for introns)

ADD REPLYlink written 3.1 years ago by abc30

Does this have to be done using biomaRt as part of a pipeline? If not you could look into the ChIPseeker package for straight-forward annotation.

ADD REPLYlink modified 6 months ago by RamRS20k • written 3.1 years ago by cbio400

No, just I need annotation base on Ensembl

ADD REPLYlink written 3.1 years ago by abc30

This package need specific input format that I don't have

ADD REPLYlink written 3.1 years ago by abc30
1

The input is a bedfile that can be read in by using the readPeakFile function, followed by the annotatePeak function. That should give you what you're looking for.

The example you've shown is basically a bedfile, so I'm not sure what the problem is.

ADD REPLYlink modified 6 months ago by RamRS20k • written 3.1 years ago by cbio400

Thanks, I face to this error

Error in file.exists(peak) : invalid 'file' argument
ADD REPLYlink modified 6 months ago by RamRS20k • written 3.1 years ago by abc30
1
gravatar for Emily_Ensembl
3.1 years ago by
Emily_Ensembl17k
EMBL-EBI
Emily_Ensembl17k wrote:

Something like:

gene_list <-getBM(
              attributes=c(
                     'ensembl_gene_id',
                     'ensembl_transcript_id'
                     ),
              filters='chromosomal_region',
              values="10:100572320:100572373:-1,10:100572649:100572658:1",
              mart = ensembl
              )
ADD COMMENTlink modified 6 months ago by RamRS20k • written 3.1 years ago by Emily_Ensembl17k

Thanks but for find intronic or exonic which attributes should be used?

ADD REPLYlink written 3.1 years ago by abc30
1

biomaRt can't work at that level of detail.

ADD REPLYlink written 3.1 years ago by Emily_Ensembl17k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1195 users visited in the last hour