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Thread | Thread Starter | Forum | Replies | Last Post |
RNA-Seq: Recent Applications of DNA Sequencing Technologies in Food, Nutrition and Ag | Newsbot! | Literature Watch | 0 | 08-23-2011 03:00 AM |
ChIP-Seq: RSAT 2011: regulatory sequence analysis tools. | Newsbot! | Literature Watch | 0 | 08-17-2011 03:00 AM |
ChIP-Seq: ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expre | Newsbot! | Literature Watch | 0 | 05-19-2011 03:50 AM |
ChIP-Seq: ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysi | Newsbot! | Literature Watch | 0 | 03-02-2011 03:50 AM |
ChIP-Seq: ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip dat | Newsbot! | Literature Watch | 0 | 05-13-2010 03:00 AM |
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#1 |
--Site Admin--
Location: SF Bay Area, CA, USA Join Date: Oct 2007
Posts: 1,358
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Seems I can't go a week without finding a paper describing a new ChIP-Seq analytical tool, so I thought it would be helpful to put together a list of a few of the most interesting papers in this area.
For those not familiar with ChIP-Seq, it involves massively parallel sequencing of nucleic acids recovered from a chromatin-immunoprecipitation (ChIP). ChIP uses an antibody to capture protein that has been previously crosslinked to DNA in its native state. Thus, ChIP-Seq allows sequencing of all DNA that a specific protein physically interacts with within the cell. There are quite a few studies recently which describe either a software tool, and/or an analytical framework for working with this type of data. The difficulty and thus the plethora of approaches is using the read density information to "call peaks" or more precisely, statistically significant ChIP-Seq binding sites. Recent papers I have found helpful are below, in reverse chronological order. Please accept my apologies in advance if I've missed your favorite tool. November
October
September
August
Hopefully those are useful. I'll post up my experiences with some of these tools soon, and would love to hear yours. |
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#2 |
Director at CLC bio
Location: Denmark Join Date: Aug 2008
Posts: 26
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What a great list - thanks a lot for posting!
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#4 |
Senior Member
Location: Vancouver, Canada Join Date: Feb 2008
Posts: 236
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Hey ECO,
Awesome list, I can't believe how many people there are writing ChIP-Seq software, now. At any rate, this is a great resource for people just getting into the field. (= Can I ask that you put a link to the FindPeaks 3.2 homepage, now? I've already got pre-compiled jar files up on the web, so maybe it's time to start pointing people in that direction (= http://vancouvershortr.sourceforge.net/ Anthony
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The more you know, the more you know you don't know. —Aristotle |
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#5 |
Member
Location: South East Asia Join Date: Nov 2008
Posts: 44
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Hi Eco,
Great list. BTW, do you happen to know any literature that does the error correction model of tag counts. |
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#6 |
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Location: SLC, Utah Join Date: Jun 2008
Posts: 60
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Here's our publication, it's finally out:
http://www.biomedcentral.com/1471-2105/9/523/abstract And the project web site: http://useq.sourceforge.net/ I'd like to suggest running a bake off using some simulated spike-in data until real spike-in data becomes available. This was critical for evaluating the methods used in the USeq package. Basically add simulated spikes to real input DNA sequencing data then run your favorite software to call peaks. I'm near getting together a stranded dataset that would be a good first start. Would be nice to sweeten the pot though. Maybe we could get Illumina to throw in an iPod to the winner? |
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#7 |
Junior Member
Location: Los Angeles Join Date: Mar 2009
Posts: 8
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Bioconductor is in the process of developing an R package (appropriately labeled chipseq currently) which should be released in the not too distant future. A working version can be had from the developers subversion repository, but again its incomplete and may change over time. Conversion of Data objects is a little bit troublesome, but the mailing list can be browsed for tips on this.
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#8 |
Member
Location: Davis, CA Join Date: Mar 2009
Posts: 82
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Hi all,
Anyone have updates to this list of programs? ![]() |
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#9 |
Senior Member
Location: Vancouver, Canada Join Date: Feb 2008
Posts: 236
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I'll be updating FindPeaks (Vancouver Short Read Analysis Package) to version 4, shortly.... is there something specific you're looking for?
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The more you know, the more you know you don't know. —Aristotle |
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#10 |
Member
Location: Davis, CA Join Date: Mar 2009
Posts: 82
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Cool! Not looking for anything in particular, just trying to make sure I've checked out the different algorithms out there
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#11 |
Junior Member
Location: Poznan, Poland Join Date: Jul 2008
Posts: 6
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Hi,
In this paper, you can find other ChIP-seq algorithm. It is implemented in R http://www.pubmedcentral.nih.gov/art...?artid=2671559 The baisc idea was 1) Extend the reads and use the minimum number of read that overlap a a nucleotide position among both strnad. This is, the number of reads should be supported by the two strands independently. This is to avoid peaks that have a block shape. 2)Normalize data and sample regarding their covarage distribution 3)Use permutation to estimate the FDR control |
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#12 |
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Location: Basel, Switzerland Join Date: Feb 2009
Posts: 27
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might want to add PeakSeq too:
http://www.nature.com/nbt/journal/v2.../nbt.1518.html Not earth-shattering, but i think their advice on normalising to input is really worthwhile. |
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#13 |
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Location: Davis, CA Join Date: Mar 2009
Posts: 82
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Two new ones out there:
GLITR: http://web.me.com/kaestnerlab1/GLITR/ and TIROE: http://www.pnas.org/content/106/13/5187.abstract |
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#14 |
Junior Member
Location: Worcester MA USA Join Date: Nov 2008
Posts: 2
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Is CHiPSeq from the Wold lab not available any longer. The links seem to go nowhere.
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#15 | |
Member
Location: new york city Join Date: Apr 2009
Posts: 40
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![]() Quote:
http://woldlab.caltech.edu/rnaseq/ |
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#16 |
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Location: BEIJING, CHINA Join Date: Sep 2009
Posts: 74
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A wonderful work!!!
thank you |
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#17 |
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Location: Columbus, OH Join Date: Feb 2009
Posts: 11
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Where can I find the results that Nix suggested earlier, same sample sequences tested with different peak finding software?
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#18 |
Member
Location: SLC, Utah Join Date: Jun 2008
Posts: 60
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Here's the thread to the ChIP Seq Challenge http://seqanswers.com/forums/showthread.php?t=1039
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#19 |
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Location: Earth Join Date: Apr 2010
Posts: 34
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Hi All,
We recently completed first chip-seq run in our laboratory. We could find a few good peaks with MACS. What I want to do is find the distribution of the distances of all the genes that are closes to the peaks on their respective 5' and 3' end. Is there a simple way to do it. Naturally I have the genomic coordinates. If anybody has done this before, it will help most helpful else I will try to write a tool to get it done. regards |
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#20 |
Member
Location: Davis, CA Join Date: Mar 2009
Posts: 82
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You might want to check out the following tool, which has a built in "nearest gene finder". http://havoc.genomecenter.ucdavis.ed...in/chipseq.cgi
Cheers, Lizzy |
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