[galaxy-user] Question about megablast

2012-04-09 Thread shamsher jagat
I have a question about megablast, I want to megablast my seq:
the databases mentioned include (against target databases):
htgs27
nt27
wgs 09
phiX174

How can I find details about these databases and which one is human or
mouse or may be best for my case.


Thanks

Vasu
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-user] Tophat paired end read

2012-04-09 Thread Jennifer Jackson

Hello Jiwen,

No, you do not need to join the files for the quality processing.

Hopefully this helps!

Best,

Jen
Galaxy team

On 4/9/12 9:14 AM, 杨继文 wrote:

Hi all,
I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate
files. Before mapping, I need to trim the reads.

My questions is : Do I have to join pair end reads before timming, and
then split again for Tophat???

Lookiong forward to your answers.

Thanks

Jiwen




___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Re: [galaxy-user] Question about megablast

2012-04-09 Thread Jennifer Jackson

Hello Vasu,

These databases contain sequences from all species in the divisions. The 
number indicates the release version. The actual source is:

ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/

A description of each division's contents can be found at:
http://www.ncbi.nlm.nih.gov/genbank

The exception is this single-species genome:
http://en.wikipedia.org/wiki/Phi_X_174

Hopefully this helps,

Jen
Galaxy team

On 4/9/12 9:57 AM, shamsher jagat wrote:

I have a question about megablast, I want to megablast my seq:
the databases mentioned include (against target databases):
htgs27
nt27
wgs 09
phiX174
How can I find details about these databases and which one is human or
mouse or may be best for my case.
Thanks
Vasu


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/


Re: [galaxy-user] Tophat paired end read

2012-04-09 Thread Carlos Borroto
Jiwen, I wonder if you are thinking about the situation where you
could be discarding reads that are to short after trimming?. In that
case you could be getting the two files out of sync. If this is the
case, I think you do need to join the files first, do the trimming and
then take them apart again.


Regards,
Carlos

On Mon, Apr 9, 2012 at 1:25 PM, Jennifer Jackson j...@bx.psu.edu wrote:
 Hello Jiwen,

 No, you do not need to join the files for the quality processing.

 Hopefully this helps!

 Best,

 Jen
 Galaxy team


 On 4/9/12 9:14 AM, 杨继文 wrote:

 Hi all,
 I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate
 files. Before mapping, I need to trim the reads.

 My questions is : Do I have to join pair end reads before timming, and
 then split again for Tophat???

 Lookiong forward to your answers.

 Thanks

 Jiwen




 ___
 The Galaxy User list should be used for the discussion of
 Galaxy analysis and other features on the public server
 at usegalaxy.org.  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

 To manage your subscriptions to this and other Galaxy lists,
 please use the interface at:

   http://lists.bx.psu.edu/

 ___
 The Galaxy User list should be used for the discussion of
 Galaxy analysis and other features on the public server
 at usegalaxy.org.  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

 To manage your subscriptions to this and other Galaxy lists,
 please use the interface at:

  http://lists.bx.psu.edu/

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-user] permissions on folder created by Galaxy

2012-04-09 Thread Jennifer Jackson

Hello,

I am going to forward your question over to the galaxy-...@bx.psu.edu 
mailing list so that it can get more visibility in the development 
community. That list is probably where you will want to post regarding 
similar topics in the future:

http://wiki.g2.bx.psu.edu/Support#Mailing_Lists

To get things started, I am wondering if you are asking about datasets 
in histories or data in libraries? Parts of your question seem to refer 
to both, or I have misunderstood (my apologies!).


If about data in libraries, then you can get around this by not actually 
moving the data into the Galaxy directory structure at all, and instead 
just link in data from some other location on the filesystem (where you 
can control the permissions). See the Copy data into Galaxy? No option 
described on this wiki:

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

Other data/lib/security related links, mostly admin UI:
http://wiki.g2.bx.psu.edu/Learn/Security Features
http://wiki.g2.bx.psu.edu/Admin/Data Libraries/Libraries
http://wiki.g2.bx.psu.edu/Admin/Data Libraries/Library Security

Hopefully this helps or some more discussion on the galaxy-dev list 
about your question will find a solution,


Jen
Galaxy team

On 4/6/12 2:42 AM, Guilhem Sempéré wrote:

Hi,

I would like folders created by Galaxy under the location defined by the
file_path parameter (which defaults to database/files) to be created
with permissions 775 instead of 755. Is this possible?

The reason for me asking this question is that I have developed an
external tool (running under Tomcat) for feeding Galaxy libraries. And
my tomcat user needs to be allowed to write to the mentioned folders.

Any ideas?

G.
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

http://lists.bx.psu.edu/

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/