SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonym Newsbot! Literature Watch 1 02-27-2013 03:16 AM
RNA-Seq: Detection of splicing events and multiread locations from RNA-seq data based Newsbot! Literature Watch 0 10-26-2011 02:50 AM
RNA-Seq: Composite Transcriptome Assembly of RNA-seq data in a Sheep Model for Delaye Newsbot! Literature Watch 0 03-26-2011 02:02 AM
RNA-Seq: Length Bias Correction for RNA-seq Data in Gene Set Analyses. Newsbot! Literature Watch 0 01-22-2011 02:02 AM
RNA-Seq: SAW: A Method to Identify Splicing Events from RNA-Seq Data Based on Splicin Newsbot! Literature Watch 0 08-14-2010 02:00 AM

Reply
 
Thread Tools
Old 04-16-2009, 12:05 PM   #1
mbjohnson
Member
 
Location: Boston, MA

Join Date: Apr 2009
Posts: 15
Question browsing Cloonan et al RNA-seq data

Hi all,
I'm wondering if anyone knows a way to browse the Cloonan et al. (Nature Methods '08) RNAseq data from mouse ES/EB cells, preferably on UCSC Genome Browser?

For example, data from the Mortazavi paper is on the Wold lab website in "wiggle" format which I uploaded to UCSC genome browser with no problem. But the Cloonan paper data is in a strange (to me) format in the NCBI Short Read Archive (e.g. "ES.all.combined.positive.wig.rounded.condensed.4plus").

Does anyone know what to do with this file? The Short Read Archive doesn't seem to have any clear documentation on this....
Thanks a lot!
Matt
mbjohnson is offline   Reply With Quote
Old 06-11-2009, 02:11 AM   #2
inesdesantiago
Member
 
Location: LONDON, UNITED KINGDOM

Join Date: Jan 2009
Posts: 44
Default Cloonan et al

I have the same question! Did you find a solution in the meentime?
Regards,
Ines
inesdesantiago is offline   Reply With Quote
Old 06-24-2009, 02:45 AM   #3
n.cloonan
Junior Member
 
Location: Brisbane, Australia

Join Date: Jun 2009
Posts: 2
Default

Hi Ho,

The files in the short read archive are gzipped wiggle plots, and can be loaded into the UCSC genome browser just the same as any other wiggle plots. Hope that helps.

Cheers,
Nicole.
n.cloonan is offline   Reply With Quote
Old 06-24-2009, 02:30 PM   #4
inesdesantiago
Member
 
Location: LONDON, UNITED KINGDOM

Join Date: Jan 2009
Posts: 44
Thumbs down Cloonan et al

Hi n.cloonan,
And what about the files with raw data? I would like to compare my mappings with gene expression data.
(sorry about the icon, it is not the one I wanted, I thought it was a question mark, I can't take it out...)

Last edited by inesdesantiago; 06-24-2009 at 02:31 PM. Reason: delete icon
inesdesantiago is offline   Reply With Quote
Old 06-25-2009, 03:39 PM   #5
n.cloonan
Junior Member
 
Location: Brisbane, Australia

Join Date: Jun 2009
Posts: 2
Default

Hi Ho,

Interestingly, I recieved an email yesterday from the SRA saying that they have just loaded the data, which confused me a little because it's been accessible under that accession number for a year now. It looks like they have converted all of the raw data to fastq format, and the wiggle plots and BED junctions are no longer available from the SRA.

Information on the fastq format is here:

http://maq.sourceforge.net/fastq.shtml

URLs for the wiggle plots and BED tracks can be accessed from:

http://www.expressiongenomics.org/SQRL.html

There is no need to download those files, although of course you can. You can simply paste the URL into the UCSC genome browser. I'll be making the aligned data available for download in the next few days, so if you're looking for this check back soon.

Cheers,
Nicole.
n.cloonan 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 08:41 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO