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Old 06-16-2011, 03:24 PM   #1
RadAniba
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Default Chipseq data analysis

Hi,

I am new to Chip-Seq data analysis and I am interested in doing this kind of analysis given a genomic position range

Find enrichment in H3K4me(1 and 3)
H3K9,14Ac
P300 occupancy
DNAse activity sites
TFBS
I would like to know from where to start, which data I have to get and from where ? I've seen a lot of data in ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ but the read me file is not informative for a newbie

My second question is what are the best open source tools to use for these kind of analysis and what are the steps to follow (all the tutorials part are dealing with explaining what is chipseq and not how to analyze the data ? )

Thank you for your help
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Old 06-17-2011, 06:52 AM   #2
howi
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Do you want to analyse publicly available data or your own data? What kind of formats do you have?
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Old 06-17-2011, 07:03 AM   #3
RadAniba
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Yes I would like to analyze public available data.
I found that Braod Institute provide for a given mark (H3K4me1) for example, peaks file compressed, what kind of information do we find in these files ? (i will try to open one to see as well) Do we find the region of a given peak (from xxx to xxx) ?
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Old 06-17-2011, 07:04 AM   #4
RadAniba
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It would be nice if someone explain the significance of all files provided by Broad

bam, bam.bai, bigWig etc ...
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Old 06-17-2011, 07:08 AM   #5
RadAniba
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a peak file looks like this

Quote:
chr22 16847536 16863983 . 294 . 1.877598 12.7 -1
chr22 16850062 16850215 . 1000 . 13.626036 6.0 -1
chr22 16850752 16850925 . 1000 . 19.582503 15.4 -1
chr22 17306120 17307007 . 482 . 4.994549 6.9 -1
chr22 17394530 17395284 . 452 . 4.493068 3.2 -1
what are the columns refers to ? I can undertand the three one but after ?
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Old 06-17-2011, 10:29 AM   #6
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Formats: http://genome.ucsc.edu/FAQ/FAQformat.html
BAM contains mapped reads (http://samtools.sourceforge.net/).
BigWig contains the coverage made from that reads.
Peak files contain enriched regions estimated by a peak calling program (e.g. http://liulab.dfci.harvard.edu/MACS/index.html). Meaning of the columns: http://genome.ucsc.edu//cgi-bin/hgTa...e+table+schema

if u want to work with such data u need a access to a unix system and/or use http://main.g2.bx.psu.edu/.

good luck :>

Last edited by howi; 06-17-2011 at 10:33 AM.
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Old 06-17-2011, 10:35 AM   #7
RadAniba
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Thank you howi for these useful information
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