SEQanswers

Go Back   SEQanswers > Applications Forums > Epigenetics



Similar Threads
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 02:00 AM
ChIP-Seq: RSAT 2011: regulatory sequence analysis tools. Newsbot! Literature Watch 0 08-17-2011 02:00 AM
ChIP-Seq: ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expre Newsbot! Literature Watch 0 05-19-2011 02:50 AM
ChIP-Seq: ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysi Newsbot! Literature Watch 0 03-02-2011 02:50 AM
ChIP-Seq: ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip dat Newsbot! Literature Watch 0 05-13-2010 02:00 AM

Reply
 
Thread Tools
Old 11-02-2008, 11:50 PM   #1
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,352
Default A brief review of recent ChIP-Seq tools literature

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.
ECO is offline   Reply With Quote
Old 11-03-2008, 12:32 AM   #2
Roald
Director at CLC bio
 
Location: Denmark

Join Date: Aug 2008
Posts: 26
Default

What a great list - thanks a lot for posting!
Roald is offline   Reply With Quote
Old 11-04-2008, 05:37 AM   #3
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,352
Default

Just when I think I captured them all...another one comes out!

CisGenome
ECO is offline   Reply With Quote
Old 11-15-2008, 11:45 AM   #4
apfejes
Senior Member
 
Location: Oakland, California

Join Date: Feb 2008
Posts: 236
Default

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
__________________
The more you know, the more you know you don't know. —Aristotle
apfejes is offline   Reply With Quote
Old 11-18-2008, 01:31 AM   #5
foolishbrat
Member
 
Location: South East Asia

Join Date: Nov 2008
Posts: 44
Default

Hi Eco,

Great list.

BTW, do you happen to know any literature that does the error correction model of tag counts.
foolishbrat is offline   Reply With Quote
Old 12-19-2008, 09:53 AM   #6
Nix
Member
 
Location: SLC, Utah

Join Date: Jun 2008
Posts: 60
Default USeq chIP-seq package

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?
Nix is offline   Reply With Quote
Old 04-23-2009, 02:18 PM   #7
dnewkirk
Junior Member
 
Location: Los Angeles

Join Date: Mar 2009
Posts: 8
Default

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.
dnewkirk is offline   Reply With Quote
Old 05-08-2009, 04:16 PM   #8
ewilbanks
Member
 
Location: Davis, CA

Join Date: Mar 2009
Posts: 81
Default updates?

Hi all,

Anyone have updates to this list of programs?
ewilbanks is offline   Reply With Quote
Old 05-08-2009, 08:01 PM   #9
apfejes
Senior Member
 
Location: Oakland, California

Join Date: Feb 2008
Posts: 236
Default

I'll be updating FindPeaks (Vancouver Short Read Analysis Package) to version 4, shortly.... is there something specific you're looking for?
__________________
The more you know, the more you know you don't know. —Aristotle
apfejes is offline   Reply With Quote
Old 05-11-2009, 09:25 AM   #10
ewilbanks
Member
 
Location: Davis, CA

Join Date: Mar 2009
Posts: 81
Default

Cool! Not looking for anything in particular, just trying to make sure I've checked out the different algorithms out there
ewilbanks is offline   Reply With Quote
Old 05-11-2009, 10:36 PM   #11
Chema
Junior Member
 
Location: Poznan, Poland

Join Date: Jul 2008
Posts: 6
Default

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
Chema is offline   Reply With Quote
Old 06-08-2009, 03:07 AM   #12
ieuanclay
Member
 
Location: Basel, Switzerland

Join Date: Feb 2009
Posts: 27
Default

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.
ieuanclay is offline   Reply With Quote
Old 07-29-2009, 11:44 AM   #13
ewilbanks
Member
 
Location: Davis, CA

Join Date: Mar 2009
Posts: 81
Default

Two new ones out there:

GLITR: http://web.me.com/kaestnerlab1/GLITR/

and

TIROE: http://www.pnas.org/content/106/13/5187.abstract
ewilbanks is offline   Reply With Quote
Old 09-30-2009, 05:14 AM   #14
david.lapointe
Junior Member
 
Location: Worcester MA USA

Join Date: Nov 2008
Posts: 2
Default

Is CHiPSeq from the Wold lab not available any longer. The links seem to go nowhere.
david.lapointe is offline   Reply With Quote
Old 10-13-2009, 12:24 PM   #15
Nicolas
Member
 
Location: new york city

Join Date: Apr 2009
Posts: 40
Default

Quote:
Originally Posted by david.lapointe View Post
Is CHiPSeq from the Wold lab not available any longer. The links seem to go nowhere.
Is that what you are looking for?

http://woldlab.caltech.edu/rnaseq/
Nicolas is offline   Reply With Quote
Old 10-19-2009, 09:39 PM   #16
tujchl
Member
 
Location: BEIJING, CHINA

Join Date: Sep 2009
Posts: 73
Default

A wonderful work!!!
thank you
tujchl is offline   Reply With Quote
Old 11-18-2009, 09:54 AM   #17
alperyilmaz
Member
 
Location: Columbus, OH

Join Date: Feb 2009
Posts: 11
Default comparisons

Where can I find the results that Nix suggested earlier, same sample sequences tested with different peak finding software?
alperyilmaz is offline   Reply With Quote
Old 11-18-2009, 10:22 AM   #18
Nix
Member
 
Location: SLC, Utah

Join Date: Jun 2008
Posts: 60
Default

Here's the thread to the ChIP Seq Challenge http://seqanswers.com/forums/showthread.php?t=1039
Nix is offline   Reply With Quote
Old 04-25-2010, 04:09 AM   #19
sameet
Member
 
Location: Earth

Join Date: Apr 2010
Posts: 34
Default

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
sameet is offline   Reply With Quote
Old 04-26-2010, 09:29 AM   #20
ewilbanks
Member
 
Location: Davis, CA

Join Date: Mar 2009
Posts: 81
Default

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
ewilbanks is offline   Reply With Quote
Reply

Tags
chip-seq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:06 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO