What Information Does The Encode Chip-Seq Peak File Contain

Question

[Radhouane Aniba]

Hi All

A broad peak file (chip-seq) 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 referring too ? I can understand the three ones but what about the others ?

[Radhouane Aniba]

Well I got my answer from seqanswers.com, so to whome it may concerns here is the answer :

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 :>

[Weronika]

It might be good to post the information you found as an answer so that this question shows up as answered for future reference.

Answer 1

[Radhouane Aniba]

Sure weronika !

Well I got my answer from seqanswers.com, so to whome it may concerns here is the answer :

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 :>