Hi,
I am new to Chip-Seq data analysis and I am interested in doing this kind of analysis given a genomic position range
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
The ENCODE consortium makes available raw and processed data for download here. So for example to get H3K4me3 peaks in hg19 I would follow the Broad Histone link, and download all files ending in "h3k4me3stdpk.broadpeak.gz".
Make sure the data you use is past the embargo date listed on the left before you publish though.
A broad peak file looks like this
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 refering too ? I can understand the three ones but what about the others ?
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Did you want to do the peak calling yourself, or use peaks picked already by ENCODE?
If the pics are already done yes i can use them at first and then refine if needed
Also you've listed data you're interested in, but not any of the questions you're interested in.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326. doi:10.1371/journal.pcbi.1003326
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003326