Hello,

I want to retrieve the genes that are present within a series of regions. Say, I have a bed file with query positions such like:

1     2665697     4665777      MIR201
1    10391435    12391516      MIR500
1    15106831    17106911      MIR122
1    23436535    25436616      MIR234 
1    23436575    25436656      MIR488

I would like to get the genes that fall within those regions.

I have tried using biomaRt, and bedtools intersect, but the output I get, is a list of genes corresponding to all the regions, not one by one, as the desired output I would like to get would be the genes within each row, but in separate rows, a if I did one query region at a time. Basically I want to know what genes fall within each region, but still being able to identify which genes fall in which regions.

What I am doing is, from a region of detected miRNA, I am expanding the genome region upwards and downwards, so that I get the neighboring genes from this miRNA. I am using a 1 million bases windows up and down. This would work for just one query, but, how to do many queries with biomaRt or many intersections with bedtools, so that I get somewhat like:

1     2665697     4665777      MIR201      GENEX, GENEY, GENEZ...
1    10391435    12391516      MIR500      GENEA, GENEB, GENEC...
1    15106831    17106911      MIR122
1    23436535    25436616      MIR234 
1    23436575    25436656      MIR488

Meaning that GENEX, GENEY and GENEZ fall within 1:2665697-4665777, with MIR201, placed in the middle, as this region is calculated subtracting 1 million bp to sart, and adding 1 million bp to end position.

I am somewhat determining the neighboring genes from each miRNA, to compare within species, but I do not get how to query multiple regions individually using biomaRt or bedtools

Any help?