Hi Stephen and Peter,
This change is definitely possible, and because the SAM format specifies that
its quality scores are phred scaled and ASCII offset of 33 (regardless of
provided input) it shouldn't cause complications downstream. We'll add this to
our todo list. I created a ticket:
https:
Hi,
I am trying to view Converted Interval Data in GeneTrack, but all I get is
"Server Error An error occurred. See the error logs for more
information. (Turn debug on to display exception reports here)"
thx,
Felix
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Hi,
I have been trying to get reference data from the ucsc browser into Galaxy, but
when I try to get the rat genome in gtf format, I only get files halfway
through chomosome 10. This happens with both of the available builds for the
rat. I am guessing this is a problem with the UCSC files a
Hi Mike,
I was able to select fastqsanger files from one of my histories at our public
server. If you are using the public server, can you share your history with me
and I will check if there is a reason you are unable to select these datasets.
If you are trying this on your local instance, ca
Felix Hammer wrote:
> Hi,
> is it possible to use SCP to upload files instead of FTP?
Hi Felix,
At this time, no.
--nate
> thxbye,
> Felix
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> The Galaxy User list should be used for the discussion
> of Galaxy analysis and other features on the pu
Dear Peter,
Thanks for the quick reply. But yes, the groomer output was marked as
fastqsanger. I changed to generic fastq and back and it didn't work either way.
I only get the fasta files from my history as possible input files. However,
using the local installation via command line seemed to
On Thu, Feb 17, 2011 at 5:48 AM, Peter Cock wrote:
> On Thu, Feb 17, 2011 at 3:00 AM, Sean Davis wrote:
> > I have a tool that takes a pdb file as input. The authors of the
> *compiled*
> > code require that the suffix be either ".pdb" or ".ent". When I upload a
> > .pdb file, the filename that
Hi,
is it possible to use SCP to upload files instead of FTP?
thxbye,
Felix
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The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. For discussion of local Galaxy
instances a
On Thu, Feb 10, 2011 at 6:42 PM, Peter wrote:
> On Thu, Feb 10, 2011 at 6:34 PM, Stephen Taylor wrote:
>>
>> Sounds like this should be added into the main release. It would save a lot
>> of time/disk space instead of using Groomer.
>>
>
> I agree. Maybe Dan can take care of it - I don't have bowti
On Thu, Feb 17, 2011 at 3:00 AM, Sean Davis wrote:
> I have a tool that takes a pdb file as input. The authors of the *compiled*
> code require that the suffix be either ".pdb" or ".ent". When I upload a
> .pdb file, the filename that gets fed to the tool now ends in .dat. What is
> the best wa
On Thu, Feb 17, 2011 at 10:06 AM, Michael Walter
wrote:
>
> Hi List,
>
> I have a couple of miRNA-Seq files (Illumina GAIIx, 29nt read length). These
> reads contain differing amounts of 3' adapter sequences and therefore map
> really badly to the human genome (with eland v2). Therefore, I'd like
Hi List,
I have a couple of miRNA-Seq files (Illumina GAIIx, 29nt read length). These
reads contain differing amounts of 3' adapter sequences and therefore map
really badly to the human genome (with eland v2). Therefore, I'd like to use
the FastX clipper tool, which states that "This tool clip
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