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Old 12-31-2009, 01:40 AM   #1
dwb0211
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Default how to get annotation form genomic region?

I usually use CisGenome to annotate genomic regions,but here I have some promble when I want to annotation some genomic regions from mm7,because the cisgenomic don`t supply the genomic data of mm7,so i just want to known whether there are some other tool or program that could annotation the genomic region to NCBI build 35?

could somebody give me some clue?
THX!
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Old 12-31-2009, 02:02 AM   #2
dawe
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If you can get your genes into a BED file you may try BEDTools
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Old 01-03-2010, 02:52 AM   #3
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Here is my genomic binding sites, which come from the Affymetrix Mouse Tiling 2.0R Array Set, I tried the BedTool, but no idea to get the closet genes of these binding regions from MM7(MM8 and MM9 would be easy to get the results from the Cisgenome), so did there any other tools to do so?


Code:
1	chr1	3205420	3205982		
2	chr1	3411553	3412798		
3	chr1	4344542	4345066		
4	chr1	5018178	5019245		
5	chr1	6740660	6741776		
6	chr1	8452675	8453199		
7	chr1	9672954	9673580		
8	chr1	9707298	9708304		
9	chr1	9779034	9780322		
10	chr1	9887175	9887946		
11	chr1	9991291	9991997	
......
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Old 01-09-2010, 02:47 AM   #4
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would anybody give me some suggestion?
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Old 01-11-2010, 01:46 AM   #5
steven
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Not sure i understand all the problem, but i would try to get the gene annotation from the ucsc genome browser (i don't know about mm7, 8 or 9 but they propose 3 assembly versions). Then you can send it directly to galaxy, upload your positions, then use the "operate on genomic intervals" to fetch the closest ones.
Alternatively, you can download the gene annotation and process it with your file locally using bedtools.
Does this help? Let me know if you need more precise infos (if i am more or less in the good direction).
cheers,
s.
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Old 01-13-2010, 04:54 AM   #6
dwb0211
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I appreciate you very much for your help,Steven.

I want to get the closest gene of each genomic regions.
I spent some time to experience the galaxy,but I fail to fix my problem owing to not familiar with the programm.

Now I'm very confused,and need some help!

D.
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Old 01-13-2010, 05:45 AM   #7
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OK, so let's try locally then. Did you manage to get the gene annotation of the correct version of the mouse genome? Go to UCSC tables: make sure you select the same assembly than the one used in your array. Select format: BED. Then on the next page (after hitting "get output") select "Create one BED record per Whole gene".
This should give you a BED file with the boundaries of each gene: genes.bed.

Now using BEDtools (link above), try something like
closestBed -a regions.bed -b genes.bed
It should give you the closest gene for each binding region.

Does this help?
Something better, someone else?
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Old 01-13-2010, 09:35 PM   #8
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It's done, thank you so much for your help.

I get much from your help.

^_^
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