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Old 09-10-2015, 12:56 PM   #1
Location: baltimore

Join Date: Oct 2009
Posts: 89
Default get genes located in a genomic region


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.
adrian is offline   Reply With Quote
Old 09-10-2015, 01:33 PM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

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.
dpryan is offline   Reply With Quote
Old 09-12-2015, 08:21 PM   #3
Senior Member
Location: chicago

Join Date: Jul 2012
Posts: 351

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.
cmccabe is offline   Reply With Quote

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