Thanks David,
I had considered this possibility but, curiously, the files don't show up in
the FastQ Groomer pull-down menu either. The original (multiplexed) data
file that I split using the Barcode Splitter is there (and, incidentally, I
ran FastQ Groomer on that before doing the barcode split), but none of the 3
files resulting from the splitter show up. Any other thoughts? It seems like
the new files just aren't landing in my history, though I can look at them
by clicking their links from the Barcode Splitter output.
Jeremy

On Mon, Jul 18, 2011 at 12:01 PM, David K Crossman <dkcro...@uab.edu> wrote:

> Jeremy,****
>
> ** **
>
>                 The files need to be groomed using the FastQ Groomer so
> that they will end up in the fastqsanger state.  Then your files will show
> up in the pull-down menus.****
>
> ** **
>
> David****
>
> ** **
>
> ** **
>
> *From:* galaxy-user-boun...@lists.bx.psu.edu [mailto:
> galaxy-user-boun...@lists.bx.psu.edu] *On Behalf Of *Jeremy Coate
> *Sent:* Monday, July 18, 2011 1:44 PM
> *To:* galaxy-user@lists.bx.psu.edu
> *Subject:* [galaxy-user] using files produced by "Barcode Splitter"****
>
> ** **
>
> I used the "Barcode Splitter" tool to split multiplexed RNA-Seq libraries
> into separate files. I would now like to map the reads from each of these
> fastq files to a reference genome. However, the fastq files generated by
> Barcode Splitter don't appear in the "Fastq File" pull-down menus within the
> the BWA or Bowtie launch pages. I'm probably missing something obvious, but
> what is the trick for making these files available for the mapping tools? Do
> I need to import them into my history somehow?****
>
> ** **
>
> Thanks!
> Jeremy****
>
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