Maya,
Many tools require that fastq files specify that they are of sanger quality
score. Specifically, "Map with BWA for Illumina", etc. If you click the
pencil icon ("Edit Attributes") on your uploaded dataset and change the data
type from 'fastq' to 'fastqsanger', you should be able to run
Hello,
I uploaded a couple fastq files to Galaxy (Illumina GA2X sequencer).
The files uploaded successfully and are green in the history section.
However, neither file is visible in the drop down menus for any of the
tools. I'd appreciate your help with this.
Thank you,
Maya
_
On Thu, Nov 10, 2011 at 6:10 PM, Rena Zheng wrote:
> Hi,
> I uploaded a bed file to Galaxy and did some text manipulations. I want
> to download the new file as a bed format that I can then open up in excel
> or a text editor. However, when I save the data, it is a .tabular format that
> I canno
Hi,
I uploaded a bed file to Galaxy and did some text manipulations. I want to
download the new file as a bed format that I can then open up in excel or a
text editor. However, when I save the data, it is a .tabular format that I
cannot open with these programs. What should I do?
Thanks,
Ren
Hello Everyone,
> Galaxy tells me to "cite Blankenberg D, et al. In preparation."
I think in general you should make sure to cite the authors of the
original publication in addition to Galaxy, the note in Galaxy should
make this explicit.
Small tidbits that may be useful. There is a command line
> I think in general you should make sure to cite the authors of the
> original publication in addition to Galaxy, the note in Galaxy should
> make this explicit.
Absolutely agree, the citations are arguably the most important part. The
GeneTrack paper citation is currently listed in the help f
Hi Oren,
I am posting the answer given to the galaxy-dev mailing list below for
other users, even thought this is a development topic. Next time, please
only post to a single mailing list.
Thanks!
Jen
Galaxy team
Repost:
On Nov 10, 2011, at 11:41 AM, Oren Livne wrote:
> Dear Nate,
>
> Tha
Hi Steffi,
GeneTrack should be working again on the Main server, thanks for reporting the
error.
For information on the inner workings of GeneTrack, you should consult the
paper that you mentioned, along with http://genetrack.bx.psu.edu/ and you can
additionally contact the GeneTrack author, w
Hi everybody,
I'm using the Genetrack-Peak-Predictor to predict nucleosome positions.
I still have some questions:
1) Am I correct that the genetrack indexer seems to be down on the
Public Galaxy Server? I get a server error, when I start it.
(The Genetrack Browser doesn't work either; although
I am trying to compare two genetically different strains that I have
sequenced using SOLiD. I was trying to ask where these two strains are
different, either in terms of deletions or polymorphisms, and one idea I
had was to use Bowtie to create an index from one of these strains and then
to map my
Dear All,
Is it possible to delete a galaxy user or multiple users with a UI call
or an API call?
Thanks,
Oren
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