RNA-Seq: ENCODE whole-genome data in the UCSC genome browser (2011 update).

Newsbot! · 11-03-2010, 03:00 AM

Syndicated from PubMed RSS Feeds

Related Articles ENCODE whole-genome data in the UCSC genome browser (2011 update).

Nucleic Acids Res. 2010 Oct 30;

Authors: Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ

The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (http://genome.ucsc.edu/). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC (http://encodeproject.org/) provides information about the ENCODE data and links for access.

PMID: 21037257 [PubMed - as supplied by publisher]

More...

hsmart · 11-24-2010, 02:08 PM

Dear All,

We generated ChIP-seq and RNA-seq data few cell-lines. I want to visualize these data in UCSC Genome Browser. How can I make appropriate files similar to ENCODE density plots for ChIP-seq data?
http://genome.ucsc.edu/cgi-bin/hgTra...gsid=173185756

Should I include all the reads or only reads after peak finding software?

Thanks for your help,

Best wishes,

Rakesh

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Why is it necessary to visualize the RNA-seq data in a genome browser?	pinki999	Bioinformatics	4	08-05-2013 09:13 AM
UCSC genome browser download	ashwatha	Bioinformatics	3	07-25-2011 08:58 PM
Adding NGS data to the UCSC genome browser	aer	General	18	06-27-2011 07:43 AM
UCSC Genome Browser	ECHo	Illumina/Solexa	0	02-25-2010 08:21 PM
Local UCSC genome browser server	baohua100	Bioinformatics	1	08-16-2009 04:10 PM

11-03-2010, 03:00 AM	#1
Newsbot! RSS Posting Maniac Join Date: Feb 2008 Posts: 1,443	RNA-Seq: ENCODE whole-genome data in the UCSC genome browser (2011 update). Syndicated from PubMed RSS Feeds Related Articles ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 2010 Oct 30; Authors: Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (http://genome.ucsc.edu/). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC (http://encodeproject.org/) provides information about the ENCODE data and links for access. PMID: 21037257 [PubMed - as supplied by publisher] More...

11-24-2010, 02:08 PM	#2
hsmart Member Location: Maryland Join Date: Dec 2009 Posts: 15	Dear All, We generated ChIP-seq and RNA-seq data few cell-lines. I want to visualize these data in UCSC Genome Browser. How can I make appropriate files similar to ENCODE density plots for ChIP-seq data? http://genome.ucsc.edu/cgi-bin/hgTra...gsid=173185756 Should I include all the reads or only reads after peak finding software? Thanks for your help, Best wishes, Rakesh