Software for determining Genes near peaks?

chariko · 07-07-2010, 08:03 AM

Hi all,

I am interested in getting the list of genes near to my peaks. I have tried different packages but they only give you the nearest gene to your peak. I would be interested in getting a software in which you could get alll the genes up to a distance determined by me.

Does anybody know whether this exits?

Thanks in advance

kopi-o · 07-07-2010, 08:12 AM

There are lots. For example, BEDTools (windowBED) and cisGenome. The online tool Galaxy also has this kind of functionality.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
recomend a software to detect splice sites on plant genes?	bbsinfo	Bioinformatics	0	01-06-2012 08:55 AM
Comparing input peaks to IP peaks	biznatch	Epigenetics	2	09-24-2011 12:38 PM
Peaks vs. Genes	GERALD	Bioinformatics	3	09-19-2011 07:07 AM
Determining differential expression	swarbre	Bioinformatics	0	11-12-2010 10:38 AM

07-07-2010, 08:03 AM	#1
chariko Member Location: Spain Join Date: Jun 2010 Posts: 56	Software for determining Genes near peaks? Hi all, I am interested in getting the list of genes near to my peaks. I have tried different packages but they only give you the nearest gene to your peak. I would be interested in getting a software in which you could get alll the genes up to a distance determined by me. Does anybody know whether this exits? Thanks in advance

07-07-2010, 08:12 AM	#2
kopi-o Senior Member Location: Stockholm, Sweden Join Date: Feb 2008 Posts: 319	There are lots. For example, BEDTools (windowBED) and cisGenome. The online tool Galaxy also has this kind of functionality.