browsing Cloonan et al RNA-seq data

[mbjohnson]

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]

Cloonan et al

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

[n.cloonan]

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]

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...)

[n.cloonan]

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.