asalatai@imbb.forth.gr
 spiliana@imbb.forth.gr
 

Dear all,

please find attached a description of the
ChIPseq experiment analysis, prepared by Vangelis Harokopos and updated by me.

The peak-finding results are at:

-Original samples:
http://genomics-lab.fleming.gr/fleming/external/Spilianakis/run317/D-vs-I/test_peaks.csv
http://genomics-lab.fleming.gr/fleming/external/Spilianakis/run317/G-vs-I/test_peaks.csv
http://genomics-lab.fleming.gr/fleming/external/Spilianakis/run317/S-vs-I/test_peaks.csv

-Re-run sampes:
http://genomics-lab.fleming.gr/fleming/external/Spilianakis/run317/D_r-vs-I_r/test_peaks.csv

-Union of original and re-run samples:
http://genomics-lab.fleming.gr/fleming/external/Spilianakis/run317/D_and_D_r-vs-I_and_I_r/test_peaks.csv

The format of the file is described at:
https://github.com/taoliu/MACS
From there:
test_peaks.csv is a tabular file which contains information about called peaks. You can open it in excel and sort/filter using excel functions. Information include:

chromosome name
start position of peak
end position of peak
length of peak region
absolute peak summit position
pileup height at peak summit, -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then this value should be 10)
fold enrichment for this peak summit against random Poisson distribution with local lambda, -log10(qvalue) at peak summit

We are at your disposal for any additional information.

Best wishes,
Martin

--
Dr. Martin Reczko
Head of Genomic Bioinformatics
Functional Genomics Laboratory and Genomics Facility
Institute of Molecular Biology and Genetics
Biomedical Sciences Research Center "Alexander Fleming"
Technical Coordinator - ELIXIR Greece
P.O. Box 74145
16602, Varkiza, Greece
Tel. +30-210-9656310
FAX: +30-210-9653934
email: reczko@fleming.gr






Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li, X Shirley Liu
Model-based Analysis of ChIP-Seq (MACS)
Genome Biology20089:R137
DOI: 10.1186/gb-2008-9-9-r137


Langmead B, Salzberg SL.
Fast gapped-read alignment with Bowtie 2.
Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.



Dear Pantelis,

at
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/external/Spilianakis/run317/hub.txt

are all tracks of Dr. Spilianakis,
normalized to the smallest library
BSC1r-D with 	11661275 reads.

BW,
Martin



BSC1-D.bam 	14892170
BSC1r-D.bam	11661275
BSC2-S.bam 	14022547
BSC3-G.bam 	14267251
BSC4-I.bam 	29402857
BSC4r-I.bam	21231986