Hello,
The quickest way to use a genome that is not already indexed is to load
it into you history and select it as a custom genome from the TopHat
tool form with the option:
"Will you select a reference genome from your history or use a built-in
index?:" -> "Use one from the history"
Inst
Does anyone know what happened to the chip-seq exercise by James?
It was part of a collection here:
http://main.g2.bx.psu.edu/u/james/p/exercises
and it was linked here:
http://main.g2.bx.psu.edu/u/james/p/exercise-chip-seq
But is it 'Not Found'.
It was a very useful exercise. Will it be back
Hello Eric,
I apologize, but I made a mistake, please see below
On 3/21/12 5:42 AM, Jennifer Jackson wrote:
Hi Eric,
On 3/19/12 4:13 PM, Eric Guo wrote:
Hi there,
I have two questions regarding alignment using Bowtie:
1. Is there a way to set the Seed Length (-l) to the full length of each
Hi,
Could galaxy include the Drosophila yakuba reference genome for use
with Tophat? It's not listed.
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Plea
hi to all
Would you please someone help me to remove my email from galaxy users list?
Thanks.
Moein
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Ple
Dear Sir/Madam,
I am a registered user of the public Galaxy Server (main). Any job I
submitted today is labeled as "Job is waiting to run" forever. The total
volume of my files is 249 mb, which is far below the quota limit of 250 gb,
and I am trying to run less than 8 jobs. Could you please let me
Hello Mark,
You can automatically install tools from any accessible Galaxy tool shed to
your local Galaxy instance. The Galaxy tool shed wiki provides all of the
information you'll need to do this. I recommend reading the entire wiki if you
haven't already done so.
http://wiki.g2.bx.psu.edu/
Hi,
This is a simple question, but I couldn't find an explicit explanation online.
How do I deploy a tool from the Galaxy toolshed to my local version of Galaxy?
Do I have to download the package and move the files into the tools/ directory,
and update the tool list, or is there an automatic wa
Hello Lyni,
Are you still having problems with your analysis?
If so, then I can point you to a few tools that can help.
- "FASTA manipulation" -> "Tabular-to-FASTA" and "FASTA-to-Tabular"
- "Text Manipulation" -> "Concatenate datasets"
- "Filter and Sort" -> "Sort"
I am not sure how many RN
Hi Eric,
On 3/19/12 4:13 PM, Eric Guo wrote:
Hi there,
I have two questions regarding alignment using Bowtie:
1. Is there a way to set the Seed Length (-l) to the full length of each
read instead of using a single Seed Length for all reads?
The seed length is a single input value for all seque
Dear Peter,
Thank you for your reply. You are right I do have all 6 parts of the nr
database on the server plus the .pal file in the same directory.
The .loc file still is:
database [build data] path
nr_01_Mar_2012 nr 15 Mar 2012 /path/on/the/server/nr_directory/nr
but the
On Wed, Mar 21, 2012 at 10:21 AM, Peter Cock wrote:
> 2012/3/21 Makis Ladoukakis :
>> Dear Galaxy users,
>>
>> I have been trying to upload a blastable database in my local instance of
>> galaxy. I have used the nr database and generated all the nhr, nin, nsq, and
>> nal files. I have also edited
Hi Makis,
here is my working nr entry:
/media/data/ncbi/blast/db/unpacked_nt/ntncbi_nt/media/data/databases/ncbi/blast/db/unpacked_nt/nt
i was not able to see if your tabs are correct. So maybe its just a
wrongly formatted loc file.
Cheers,
Bjoern
P.S. You can download preformatted blast-datab
2012/3/21 Makis Ladoukakis :
> Dear Galaxy users,
>
> I have been trying to upload a blastable database in my local instance of
> galaxy. I have used the nr database and generated all the nhr, nin, nsq, and
> nal files. I have also edited the blastdb.loc file in the
> galaxy-dist/tool-data/ directo
Dear Galaxy users,
I have been trying to upload a blastable database in my local instance of
galaxy. I have used the nr database and generated all the nhr, nin, nsq, and
nal files. I have also edited the blastdb.loc file in the
galaxy-dist/tool-data/ directory and it looks like this:
datab
15 matches
Mail list logo
