SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Publicly available strand-specific RNA-Seq data for MAQC samples? tmy1018 Bioinformatics 4 06-11-2012 09:18 PM
Publicly available strand-specific RNA-Seq data with corresponding RT-PCR data? tmy1018 Bioinformatics 2 05-01-2012 12:50 PM
Publicly available Illumina metagenomes metagUser Metagenomics 2 03-26-2012 11:16 PM
Publicly available NGS data? tldgID Bioinformatics 10 05-25-2011 02:11 PM
Real biological 454 data publicly available for benchmarking Springbok28 454 Pyrosequencing 1 11-25-2009 11:48 PM

Reply
 
Thread Tools
Old 05-21-2012, 08:59 PM   #1
bb420
Member
 
Location: MA

Join Date: Apr 2012
Posts: 14
Default Publicly available data

Hi everyone. What would be the best place to find all the published data? Really appreciated!!!!

Last edited by bb420; 09-20-2012 at 09:06 PM.
bb420 is offline   Reply With Quote
Old 05-21-2012, 09:25 PM   #2
PeteH
Member
 
Location: Melbourne

Join Date: Jun 2010
Posts: 64
Default

The NCBI's Short Read Archive is a good place to start http://www.ncbi.nlm.nih.gov/sra. You can easily search by experiment type. Be sure to read the documentation on the website as the downloads aren't in an immediately useable format and require conversion (using tools also available on the website).
Pete
PeteH is offline   Reply With Quote
Old 05-21-2012, 10:16 PM   #3
PeteH
Member
 
Location: Melbourne

Join Date: Jun 2010
Posts: 64
Default

I'm guessing you want the data in FASTQ format? If so, then read this http://www.ncbi.nlm.nih.gov/books/NB...erting_SRA_for. If you want aligned reads in SAM/BAM format then I don't believe the SRA will be much help as my understanding is that it only contains the raw data.

I'd also suggest reading the complete SRA Handbook (http://www.ncbi.nlm.nih.gov/books/NBK47528/). The SRA toolkit can be downloaded from here http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software. All this information, and more, is available on the homepage of the SRA, which I linked to in my previous post.
Pete
PeteH is offline   Reply With Quote
Old 05-25-2012, 03:53 AM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049
Default

http://sra.dnanexus.com/?result_type...show=&q=rnaseq

http://sra.dnanexus.com/?result_type...how=&q=chipseq

Quote:
Originally Posted by bb420 View Post
is there any place where i cn get published data for analysis. anything like chip-seq or rna-seq?
GenoMax is offline   Reply With Quote
Old 05-25-2012, 03:56 AM   #5
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049
Default

http://jimwatsonsequence.cshl.edu/cg...se/jwsequence/

Instructions on how to get the full data set from NCBI trace archives are at the top of the page.

Quote:
Originally Posted by bb420 View Post
Also, would you know where can i probably get the human genome data for watson's genome(or somebody else's for that matter....i think it is available publicly). Thanks a lot!
GenoMax is offline   Reply With Quote
Old 05-25-2012, 03:59 AM   #6
bb420
Member
 
Location: MA

Join Date: Apr 2012
Posts: 14
Default

Thank you very much! Appreciated!
bb420 is offline   Reply With Quote
Old 06-25-2012, 03:36 AM   #7
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049
Default

http://www.ncbi.nlm.nih.gov/bioproject/19621

Browser at JCVI: http://huref.jcvi.org/

Paper: http://www.ncbi.nlm.nih.gov/pubmed/17803354


Quote:
Originally Posted by bb420 View Post
Hi

can anyone please tell me where can i find craig venter's genome data? and also if any sort of detailed analysis(published or otherwise) is available on it
GenoMax is offline   Reply With Quote
Reply

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 07:11 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO