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Old 02-04-2009, 06:37 PM   #1
bogu0001
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Default CpG Islands vs CHIP-Seq data

Hey guys
I have CHIP-Seq data of Non Coding RNA with Accession nos, probe ids and other usual features of BED file.
I want to match the nearest CpG Islands related to the CHIP-Seq data.
The problems of mine are

1.which dataset has all the CpG islands related to my data (Human mRNAs)???
I downloaded a dataset named cpgdump12_1k (Full annotation dataset) from CpG Island database.But it doesn't have complete relevant data that match CHIP data

2.How to match the nearest CpGs to CHIP data???

PERL???????????
UNIX????????????

help would be appreciated.
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Old 02-04-2009, 07:52 PM   #2
Rao
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Wold you please explain more?
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Old 02-04-2009, 08:29 PM   #3
bogu0001
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I have CHIP-seq data of non coding RNAs in human (with chr start end and exon count and size along with probe ids, sequences and accession ids.)
I would like to know the nearest possible CpG islands along the TSS (trascriptional start sites)for my Chipseq data by comparing both
(rt now i'm downloading GC5base data from UCSC-Goldenpath-hg18)
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Old 02-05-2009, 09:30 PM   #4
Rao
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You are close to the solution...
In UCSC table browser, in regulation group, yo have track on CpG islands you may get location of islands.. based on that you can locate near one to your transcript...

click on describe table schema in table browser to get more details
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Old 02-05-2009, 09:33 PM   #5
Rao
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this link may help you

http://genome.ucsc.edu/cgi-bin/hgTab...a_outFileName=
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