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Old 02-10-2014, 11:21 AM   #1
Liy
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Location: Hungary

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Default motif genome wide

Hi all,

Can someone tell me how to get all the coordinate of a sequence motif coordinate genome wide? Prefered output is bed format.

Thanks!
L
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Old 02-11-2014, 05:25 AM   #2
TiborNagy
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It is depends on what kind of motif format do you have
Homer has a program (findKnownMotifs.pl), which use matrix, but fuzznuc (part of the Emboss package) use consensus sequence as query.
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Old 02-11-2014, 08:38 AM   #3
GenoMax
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@Liy: Just to be clear about what you are asking.

You know the motif you want to get corresponding coordinates for (genome wide) with output in BED format.
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Old 02-11-2014, 12:40 PM   #4
crazyhottommy
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Quote:
Originally Posted by Liy View Post
Hi all,

Can someone tell me how to get all the coordinate of a sequence motif coordinate genome wide? Prefered output is bed format.

Thanks!
L
You may download from here http://compbio.mit.edu/encode-motifs/
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