[Nix]

Deadline extension

Hello Folks,

Several groups have asked for an extension thus, the official submission deadline is now next Tuesday, the 10th of March. Many thanks to those that have submitted processed data and to our sponsors, Illumina and Applied Biosystems.

We still need your help (yes you) to make this a success. You might even win an iPod and get published for your efforts.

If you would, download the data and run it through one of the missing chIP-Seq packages below.

-cheers, David



Current submissions:

MACS - Mali Salmon-Divon, Tao Liu
Cisgenome - Hongkai Ji
Novel Method - John (Shouyong) Peng
Genomatix Genome Analyzer - Nancy Bretschneider
SWEMBL - Steven Wilder
ERANGE3.0 - Shirley Pepke
Partek - Justin Brown
USeq - David Nix


Missing submissions:

QuEST - http://mendel.stanford.edu/sidowlab/downloads/quest/ - [email protected]

WTD/MSP/MTC - http://compbio.med.harvard.edu/Supplements/ChIP-seq - [email protected] [email protected]

F-Seq - http://www.genome.duke.edu/labs/furey/software/fseq - [email protected]

SISSRs - http://www.rajajothi.com/sissrs/ - [email protected] [email protected]

ChromaSig - http://bioinformatics-renlab.ucsd.ed...wiki/ChromaSig - [email protected] [email protected]

ChIPDiff - http://bioinformatics.oxfordjournals...act/24/20/2344 - [email protected]

PoissonMixtureModel - http://www.biomedcentral.com/1471-2164/9/S2/S23 [email protected]

ChIP-Seq - http://www.isrec.isb-sib.ch/chipseq/ - sourceforge, contact through web form

chip-seq - R library - [email protected] [email protected]

Illumina Genome Studio - [email protected]

FindPeaks - http://vancouvershortr.sourceforge.net/ - [email protected]

[Nix]

Submissions

Posted all of the submissions to http://bioserver.hci.utah.edu/ChIPSeqSpikeIns/ . 13 in total, a great response. Will post the key on April 1st along side a preliminary analysis summary.

[Nix]

Results of the Contest

Hello Folks,

I've posted some draft results as well as the key to http://bioserver.hci.utah.edu/ChIPSeqSpikeIns/ . Comments and constructive criticism are appreciated. Should finalize this in a week.

Congrats and thanks to all the participants. -cheers, David

[jsp]

Hello David,

I saw some top 500 peak list can identify 501 key regions, and this doesn’t make any sense to me. The reason is either two key regions overlapping two much or identified peak region is too big. So I propose the following suggestions here:

1. Cleaner key regions -- for neighboring key regions with too much overlaps (for example more than 40%), they should be merged into a single key region. (A good method should be able to identify key regions with some limited amount of overlapping, and that might be the theme for Community ChIP-Seq Challenge 2.0?)

2. A more objective criteria (related to the resolution of the submitted binding regions) – take the midpoint of each identified peak region and check whether it falls within a key region. ChipMaster raised a question about submitting a list with “chr1:1-lengthOfChr1” before, and “1kb rule” still favors to results with larger peak regions.

3. The above two is to avoid cases that one peak covers two key regions, we also need to avoid the cases that a single key region is identified multiple times by small peaks (I don’t know whether this has been taken care of already).

It will be interesting to see the distribution of distances b/t the identified peak centers and their corresponding key region centers.

Please change “ParkLab” to “BPC” (which stands for binding profile construction) in the report. My lab mate published a package (spp:
http://compbio.med.harvard.edu/Supplements/ChIP-seq/) on ChIP-seq peak detection, and it performed really really well on many published real ChIP-seq data sets. I hope that my participation of this challenge with my beta version of BPC won’t mislead people to think it’s the best method from Park Lab.

Thanks for putting all these together.

Looking forward to challenge 2.0

[Nix]

JSP, you are correct there are a couple key regions in close proximity that can be intersected by one candidate, thus it is possible to hit 501 key regions in the top 500 list.

As far as I am aware folks candidate regions aren't excessively large, all under 500bp.

The number of double hits are minor and won't effect the overall results.

And no, multiple hits to the same key only count once.

I'll put together a list of the actual centers used to generate the random fragments and let those interested calculate the intersections. There are several problems with this approach, namely the observed center is not the same as the actual center since read distribution is skewed by the presence of poorly alignable repeats and low complexity regions. Which do you use? Again, I very much doubt it will change the overall results.

As for additional methods, by all means run them using the simulated data and I can add them to the charts.

[Nix]

Final report

Hello Folks,

The ChIP-Seq Challenge 1.0 is over! It's been a resounding success with 13 submissions representing 12 analysis packages. Many congrats and thanks to both the players and Illumina and Applied Biosystems for providing prizes.

The datasets, submissions, analysis, and results have been archived on SourceForge on the USeq project site under CommunityChIPSeqChallenge (https://sourceforge.net/project/show...kage_id=317544).

-cheers, David

[simulation11]

Wow...that's great posts. Thanks a lot for sharing.

simulation rachat credit

[inesdesantiago]

I would like to hear about the Chip-Seq Challenge 2.0!

[bioinfosm]

Well, there is a different one, but a chipSEQ challenge = http://camda2009.bioinformatics.northwestern.edu/

[ewilbanks]

Hi David,

This is a great resource! If we were to cite it, how would you like us to do that?

Thanks!
Lizzy

[Nix]

I would cite this thread and the archive on sourceforge via html links https://sourceforge.net/projects/use...PSeqChallenge/ .

[ewilbanks]

OK thanks!

[golharam]

Any chance someone can post a summary of the results of the challenge on here? I know this is late, but it would be interesting for others to see.

[Nix]

There are a lot of files associated with the results. I also wanted this archived so follow the link above and download the README_Report.doc.zip file for the summary.

[weigonghong]

Hello David,

I'm a new user for USeq. For ChIP-seq analysis, first step is to do genome mapping with Novoaligner. However, I can't find Novoaligner in USeq_5.6/Apps. Is NovoalignParser instead?
You gave an example for mRNA-seq by using NovoalignParser: java -Xmx1500M -jar pathToUSeq/Apps/NovoalignParser -f /Novo/Run7/
-v H_sapiens_Mar_2006 -p 20 -q 30 -r /Novo/Run7/mRNASeq/ -i -g
/Anno/Hg18/mergedUCSCKnownGenes.bed

Then I compiled this command: java -jar USeq_5.6/Apps/NovoalignParser -f /wrk/data/biomedicum_solexa-090805/s_4_sequence.txt / -v /wrk/data/genomes/homo_sapiens/dna/Homo_sapiens.NCBI36.49.dna.all_chromosomes.fasta -p 20 -q 30 -r /wrk/data/gonghong/useq –i

Then there are some dialogues coming out as below:
20.0 Posterior probability threshold
30.0 Alignment score threshold

Parsing and filtering...
/wrk/data/biomedicum_solexa-090805/s_4_sequence.txt
Problem identifing chromosome column? No '>chr' found in 1st 1000 lines?

Could you please help to figure it out what happened? I'm wet-experiment postdoc and extremely want to use USeq for ChIP-seq data analysis.

I'm looking forward to your reply.

Thanks a lot.
Gonghong