Go Back   SEQanswers > Literature Watch

Similar Threads
Thread Thread Starter Forum Replies Last Post
ChIP-Seq: PeakAnalyzer: Genome-wide annotation of chromatin binding and modification Newsbot! Literature Watch 4 01-21-2017 12:50 AM
ChIP-Seq: Identifying Differential Histone Modification Sites from ChIP-seq Data. Newsbot! Literature Watch 0 12-02-2011 05:51 AM
ChIP-Seq: GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experi Newsbot! Literature Watch 0 11-18-2010 03:20 AM
ChIP-Seq: Processing and analyzing ChIP-seq data: from short reads to regulatory inte Newsbot! Literature Watch 0 09-24-2010 03:10 AM
PubMed: An integrated software system for analyzing ChIP-chip and ChIP-seq data. Newsbot! Literature Watch 0 11-04-2008 06:03 AM

Thread Tools
Old 02-07-2012, 03:00 AM   #1
RSS Posting Maniac

Join Date: Feb 2008
Posts: 1,443
Default ChIP-Seq: Picking ChIP-seq peak detectors for analyzing chromatin modification experi

Syndicated from PubMed RSS Feeds

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments.

Nucleic Acids Res. 2012 Feb 3;

Authors: Micsinai M, Parisi F, Strino F, Asp P, Dynlacht BD, Kluger Y

Numerous algorithms have been developed to analyze ChIP-Seq data. However, the complexity of analyzing diverse patterns of ChIP-Seq signals, especially for epigenetic marks, still calls for the development of new algorithms and objective comparisons of existing methods. We developed Qeseq, an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length. To objectively assess its performance relative to other 14 ChIP-Seq peak finders, we designed a novel protocol based on Validation Discriminant Analysis (VDA) to optimally select validation sites and generated two validation datasets, which are the most comprehensive to date for algorithmic benchmarking of key epigenetic marks. In addition, we systematically explored a total of 315 diverse parameter configurations from these algorithms and found that typically optimal parameters in one dataset do not generalize to other datasets. Nevertheless, default parameters show the most stable performance, suggesting that they should be used. This study also provides a reproducible and generalizable methodology for unbiased comparative analysis of high-throughput sequencing tools that can facilitate future algorithmic development.

PMID: 22307239 [PubMed - as supplied by publisher]

Newsbot! is offline   Reply With Quote
Old 06-14-2012, 05:31 AM   #2
Location: Milano, Italy

Join Date: Aug 2011
Posts: 93

someone ever tried qeseq form chip-seq analysis?
any feedback compare to MACS or SICER?

Last edited by paolo.kunder; 06-19-2012 at 02:10 AM.
paolo.kunder is offline   Reply With Quote

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 07:39 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO