Default Upstream_Flank Value Used In Getbm() In Biomart

Question

[Wenhua]

When using BioMart/getBM function to find gene annotations for SNPs without specifying upsteam_flank, the function will return the nearest genes as far as I understand. But I can't find any information about how far (e.g. 20 bp or 100 bp) the function search by default. Does anyone know what the default values the function use in that aspect? Thanks in advance.

Answer 1

[Neilfws]

Not sure that the function "will return the nearest genes". Flank (upstream or downstream) is generally used to return sequence.

If you use BioMart via the web and examine the source code of a page with form inputs to specify flank size, you see this:

<input type="text" 
 name="hsapiens_gene_ensembl__sequences__attributefilter.downstream_flank" 
 value="100" 
 onblur="if(filterEltHasValue(this)) {     
 checkAttributeCheckbox('hsapiens_gene_ensembl__sequences__attribute.downstream_flank');
};">

Which suggests that for the web version at least, the default value is 100.

[Mary]

Yeah, that's what the web interface shows. But it's not selected by default.