Geneid between regions of chromosome

Question

[tothepoint]

I am having similar query Ids between regions. For small batches the stack overflow approach works fine but if I want to print with large list it ends up with different errors. such: "failed to load http resource", "Failed to load external entity". I am fixing one other error arise.

Is there a way either using vep, biomaRt of python based by which I can fetch details. Or can we loop the program in R to get output in small batches? I am using sscrofa as my reference. My data look like :

<chr>   <start>   <end>
1       10000      20000
1       25000     350000
.        .        .
.        .        .
.        .        .
1      1000000    1001000

Thanks

Answer 1

[Ben Moore]

Hi devarora,

I would suggest using the GET overlap/region/:species/:region endpoint from the Ensembl REST API: http://rest.ensembl.org/documentation/info/overlap_region

You can only query a single region at a time using this endpoint, so you will need to create a loop to query each region of interest.

As you mentioned, BioMart can be used for this type of query, but is not a suitable tool for large, genome-wide queries.

Best wishes

Ben