Dear Malito,
I am PhD student and I am working with a bacterial transcriptome.
A few days ago, i have a problem to obtain data in DESeq and Edge-r on the
plataform galaxy.
I get the message no peek at the end of the process, even with the task g
reen.
Have you had this problem?
I would like to
Hello,
Thanks for your response. I can almost never get anything done on the
public instance of Galaxy. It can take an entire day to even load a.bed
file. When I was encountering the error I was on the Broad Instance.
Marco, I tried following the instructions above to ensure that genome was
Toni,
As a quick work-around until set up natively, you may be able to use the
Extract DNA tool with a custom reference genome:
http://wiki.galaxyproject.org/Support#Custom_reference_genome
See the example in: Tools on the Main server, should work on any
Galaxy set up as a production server
Hello,
I'm trying to convert a .bed file to a FASTA file. I get the following
error when I do.
An error occurred with this dataset: *No sequences are available for
'sacCer2', request them by reporting this error.*
I'm not sure what the issue is?
Thanks,
Toni
--
Toni Marie Delorey
Regev Lab,
Hi Toni,
to convert a bed file to a fasta file you need the genomic sequence. You
can specify a genome-build for every bed file in your history. You
probably don't have a genome build specified or its specified as
sacCer2. sacCer2 is not configured I would guess, so no genome is
available. Try to
Hi Toni,
Bjoern is correct - if you are using a local Galaxy that does not have
this reference genome available, it needs to be added. The Extract DNA
tool requires a .2bit version of the genome available and the
alignseq.loc file configured. More is here, section LASTZ and EXTRACT
Genomic
Hello,
I'm using the main galaxy server to analyse some data and then I got this
messege:
An error occurred while getting updates from the server. Please contact a
Galaxy administrator if the problem persists.
I was uploading data from my computer since yesterday morning and it seems to
take
Hello Delong ZHOU,
On 6/7/13 8:23 AM, Delong, Zhou wrote:
Hello,
I'm using the main galaxy server to analyse some data and then I got
this messege:
An error occurred while getting updates from the server. Please
contact a Galaxy administrator if the problem persists.
This message indicates
Hello,
I'm new to Galaxy.
When I read in a fasta file to Galaxy and then try to use it (in a blast
search) as the query sequence, I get the error message below, although
the uploaded fasta file is present in the history. Can anyone tell me
what the problem could be? Is there some other step I
Hello Kenneth,
Are you using BLAST+ in a local install or cloud instance? The problem
may be that the query dataset needs to have the datatype assigned as
fasta. To do this, click on the pencil icon for the dataset to reach
the Edit Attributes form. Then either scroll down to (or click on the
Hi Kenneth,
Yes, target databases require indexes and *.loc file set-up. Please see
this wiki for details. For Genbank data such as NR, FTP the pre-built
indexes and use those (generating them with formatdb is not necessary).
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
See the
Hi Kenneth,
It is likely that the path is wrong in the .loc file. It has to point to
the actual files, not just the directory. Inside here
/9720/genome_references/ncbi/nr-protein-db
is where all the nr.* files are? In that case, the path should be
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