browsing Cloonan et al RNA-seq data

mbjohnson · 04-16-2009, 01:05 PM

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

inesdesantiago · 06-11-2009, 03:11 AM

I have the same question! Did you find a solution in the meentime?
Regards,
Ines

n.cloonan · 06-24-2009, 03:45 AM

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.

inesdesantiago · 06-24-2009, 03:30 PM

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...)

n.cloonan · 06-25-2009, 04:39 PM

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.

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 04:16 AM
RNA-Seq: Detection of splicing events and multiread locations from RNA-seq data based	Newsbot!	Literature Watch	0	10-26-2011 03:50 AM
RNA-Seq: Composite Transcriptome Assembly of RNA-seq data in a Sheep Model for Delaye	Newsbot!	Literature Watch	0	03-26-2011 03:02 AM
RNA-Seq: Length Bias Correction for RNA-seq Data in Gene Set Analyses.	Newsbot!	Literature Watch	0	01-22-2011 03:02 AM
RNA-Seq: SAW: A Method to Identify Splicing Events from RNA-Seq Data Based on Splicin	Newsbot!	Literature Watch	0	08-14-2010 03:00 AM

04-16-2009, 01:05 PM	#1
mbjohnson Member Location: Boston, MA Join Date: Apr 2009 Posts: 15	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

06-11-2009, 03:11 AM	#2
inesdesantiago Member Location: LONDON, UNITED KINGDOM Join Date: Jan 2009 Posts: 44	Cloonan et al I have the same question! Did you find a solution in the meentime? Regards, Ines

06-24-2009, 03:30 PM	#4
inesdesantiago Member Location: LONDON, UNITED KINGDOM Join Date: Jan 2009 Posts: 44	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 03:31 PM. Reason: delete icon

06-24-2009, 03:45 AM	#3
n.cloonan Junior Member Location: Brisbane, Australia Join Date: Jun 2009 Posts: 2	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.

06-25-2009, 04:39 PM	#5
n.cloonan Junior Member Location: Brisbane, Australia Join Date: Jun 2009 Posts: 2	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.