get genes located in a genomic region

[adrian]

Hello:

I have a bed file of genomic coordinates in a file (# of rows in this file are 800).

chr5 87956489 87957187
chr16 89626644 89627869
chr17 72270301 72270512
chr8 2078049 2078427


I want to find all the genes in every coordinate.
I could use UCSC table browser by uploading these coordinates and select variables from tables.

However, UCSC browser allows only 1000 one at a time and I don't want to do copy paste or break file 8 times.

Is there any alternative way.

I apologize in advance in case if you suggest Biomart - I tried and I have no success there.

thanks a lot.

[dpryan]

What's wrong with breaking a file up into chunks? It's not like it takes more than a second to do. You could always use bedtools or even R if you prefer.

[cmccabe]

You could also use bedops and gencode as well. The gtf from gencode would give you the genes and bedops would give you all the gene overlaps with your bed.