how I would install it in my history?
Thanks for your help.
Sincerely,
Jeremy Coate
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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
t
** **
>
> *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 Split
into the upload
> tools URL textarea.
>
> Ideally, it would be nice for the tool developer to be able to include a
> link in the html that would "promote" the file to a dataset in the current
> history.
>
> JJ
>
>
> On 7/19/11 3:08 PM, Jeremy Coate wr
My apologies if this has been covered before but I am using Galaxy Main and
wonder if, when running TopHat, you can modify the mapping parameters used
by Bowtie? It seems that the full parameter list for TopHat pertains only
to the reads that aren't mapped by Bowtie (the reads spanning splice
junct
Hi Jeremy,
Thanks for your help. I'm mapping reads from one organism to a related but
different organism, so some of the parameters I'd like to adjust are to
relax mapping stringency -specifically:
-n 3 (allow 3 mismatches in seed)
-e 250 (allow cummulative phred score of 250 [or some other value
Hi all,
FYI, I've gotten the same error recently when trying to run Bowtie (using
Galaxy Main).
Jeremy
On Tue, May 1, 2012 at 4:37 PM, Richard Mark White wrote:
> Hi,
> Ive been trying to run cufflinks/cuffdiff but keep getting this error: Job
> output not returned by PBS: the output datasets wer
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