closed

On 3/28/11 7:38 AM, Brian Lam wrote:



galaxy-user-requ...@lists.bx.psu.edu wrote:

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Today's Topics:

   1. Convert SOLiD data (lishiyong)
   2. Re: biomart plugin (Greg Von Kuster)
   3. Re: Convert SOLiD data (Ryan Golhar)
   4. Re: Convert SOLiD data (Jennifer Jackson)
   5. Re: Sort&  index SAM-files automatically (Ryan Golhar)


----------------------------------------------------------------------

Message: 1
Date: Mon, 28 Mar 2011 11:35:15 +0800
From: "lishiyong"<lishiy...@genomics.org.cn>
To: "galaxy-user"<galaxy-user@lists.bx.psu.edu>
Subject: [galaxy-user] Convert SOLiD data
Message-ID:<201103281135102031...@genomics.org.cn>
Content-Type: text/plain; charset="us-ascii"

Hello!
       I convert SOLiD csfasta- and qual-files to fastq-files ,I want  to use 
the fastq-files to do denovo with SOAPdenovo.because the SOLiD de novo 
accessory tools Require large memory .But ,I find that there're some question 
for the converting .
for example:
T02023221102101032002002030011232121133222233311200 ��>  
AGAGTGGCCAGCACATGAAGAAGATAACCGTGCGCCTTGGGGTTTCCGAA

But I think it should to be TCCTAGACAAGTTGGCTTTCCCTTAAACAGCTGACATAGAGATATGTCCC  
Who knows the reason about this.
2011-03-28



lishiyong
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Message: 2
Date: Mon, 28 Mar 2011 08:57:49 -0400
From: Greg Von Kuster<g...@bx.psu.edu>
To: Andrea Edwards<edwar...@cs.man.ac.uk>
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] biomart plugin
Message-ID:<a3348bc1-7c00-4b8a-9313-de8444f44...@bx.psu.edu>
Content-Type: text/plain; charset="us-ascii"

Hello Andrea,

Make a copy of the ~/tools/data_source/biomart.xml for your local biomart 
install, and change the action in the following tag to point to it.

<inputs action="http://www.biomart.org/biomart/martview"; check_values="false" method="get" 
target="_top">

Then add your new biomart tool wrapper to your tool_conf.xml file and start up 
your Galaxy instance.

For details about adding a new tool, see 
https://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial.

Greg Von Kuster

On Mar 26, 2011, at 10:19 AM, Andrea Edwards wrote:

Hello

I have looked at the biomart plugin for Galaxy and this seems to allow access 
to marts on the biomart central server.
Is there anyway to use this plugin to access a biomart on my server if I can't 
make my biomart available on the biomart central server.

If not, would it be possible to achieve this with galaxy tools. I've heard of 
galaxy tools but never made one so I don;t know what is involved.

Failing that would i be able to use the biomart plugin to access my server if I 
had a local installation of galaxy


thanks
___________________________________________________________
The Galaxy User list should be used for the discussion of
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Greg Von Kuster
Galaxy Development Team
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Message: 3
Date: Mon, 28 Mar 2011 09:53:56 -0400
From: Ryan Golhar<golha...@umdnj.edu>
To: lishiyong<lishiy...@genomics.org.cn>
Cc: galaxy-user<galaxy-user@lists.bx.psu.edu>
Subject: Re: [galaxy-user] Convert SOLiD data
Message-ID:<4d9092f4.9040...@umdnj.edu>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"

Lishiyong,

You should not convert colorspace to base space prior to aligning reads.
  The reason for this is that if there is an error in one of the color
calls, it will effect all the downstream color calls.

Instead, you should use an aligner that will do the assembly in
color-space instead.  I know there are a few out there, but don't know
them off the top of my head.

Ryan

On 3/27/11 11:35 PM, lishiyong wrote:
Hello!

I convert SOLiD csfasta- and qual-files to fastq-files ,I want to use
the fastq-files to do denovo with *SOAPdenovo*.because the SOLiD de novo
accessory tools Require large memory .But ,I find that there're some
question for the converting .

for example:

T02023221102101032002002030011232121133222233311200 ??>
AGAGTGGCCAGCACATGAAGAAGATAACCGTGCGCCTTGGGGTTTCCGAA
But I think it should to be
TCCTAGACAAGTTGGCTTTCCCTTAAACAGCTGACATAGAGATATGTCCC Who knows the reason
about this.
2011-03-28
------------------------------------------------------------------------
lishiyong



___________________________________________________________
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/

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Message: 4
Date: Mon, 28 Mar 2011 06:57:06 -0700
From: Jennifer Jackson<j...@bx.psu.edu>
To: lishiyong<lishiy...@genomics.org.cn>
Cc: galaxy-user<galaxy-user@lists.bx.psu.edu>
Subject: Re: [galaxy-user] Convert SOLiD data
Message-ID:<4d9093b2.6090...@bx.psu.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hello Lishiyong,

Just to confirm, the conversion was performed at Galaxy main using "NGS:
QC and manipulation ->  Convert SOLiD output to fastq"? With the option
"double encode = yes"? If so, the output appears to be correct.

quote from tool help:

"Double encode? - converts color calls (0123.) to pseudo-nucleotides
(ACGTN). Not necessary for bowtie. Required for BWA."

Please let us know if we can help more,

Best,

Jen
Galaxy team

On 3/27/11 8:35 PM, lishiyong wrote:
Hello!

I convert SOLiD csfasta- and qual-files to fastq-files ,I want to use
the fastq-files to do denovo with *SOAPdenovo*.because the SOLiD de novo
accessory tools Require large memory .But ,I find that there're some
question for the converting .

for example:

T02023221102101032002002030011232121133222233311200 ??>
AGAGTGGCCAGCACATGAAGAAGATAACCGTGCGCCTTGGGGTTTCCGAA
But I think it should to be
TCCTAGACAAGTTGGCTTTCCCTTAAACAGCTGACATAGAGATATGTCCC Who knows the reason
about this.
2011-03-28
------------------------------------------------------------------------
lishiyong



___________________________________________________________
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/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org


------------------------------

Message: 5
Date: Mon, 28 Mar 2011 09:56:51 -0400
From: Ryan Golhar<golha...@umdnj.edu>
To: j.seggew...@ifg.uni-muenster.de
Cc: galaxy-user@lists.bx.psu.edu, Jochen Seggewi?
        <jochen.seggew...@ifg.uni-muenster.de>
Subject: Re: [galaxy-user] Sort&  index SAM-files automatically
Message-ID:<4d9093a3.5040...@umdnj.edu>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"

Jo,

Use the SAM Tools SAM-TO-BAM tool in Galaxy to convert your SAM file to
a BAM file.

Ryan


On 3/25/11 10:35 AM, Jochen Seggewi? wrote:
Hi!

Thank you for your reply.

So that means, I should convert the csfasta&  qual to fastq, map it with
Bowtie, get an SAM, convert it to BAM and then index that BAM?
How can I index BAM using GALAXY?
I haven?t found a way to get a BAM directly from GALAXY using csfasta&
qual as input files.

Best regards

Jo

Am 3/25/2011 3:13 PM, schrieb Jim Robinson:
Hi Jo,

To short-circuit confusion I'll jump in here.  I'm the developer of
IGV and igvtools,  the sorting and indexing for SAM files was added
long ago, even before indexed BAM files were possible from Java
programs.   The recommendation now is to convert to BAM and index
that,  although SAM files still work.   If the galaxy community would
like the SAM option I'm happy to have igvtools wrapped as a module,
and will help with that.

BTW,  I also have some code (xml) to wrap IGV itself as a Galaxy
visualizer,  contributed to me by a user.  As I don't have a private
Galaxy installation I'm unable to test it myself, but can make it
available if anyone is interested.

Jim


Hello!

I convert SOLiD csfasta- and qual-files to fastq-files and map those
against Hg19 (Bowtie).
I would like to use the resulting sam-files in the IGV browser (Broad
Institute).
Therefore, the sam-file need to be sorted an indexed. This could be
done using the ?igvtools?.
However, it would be nicer if this sorting and indexing could be done
automatically using GALAXY.
I guess that it is certainly possible ? but I do not know how.
Could anybody let me know how it works and what function I have to
use, respectively?
How can I sort the sam-file the correct way?

Thank you in advance.

Best regards

Jo
___________________________________________________________
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
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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/

--
CONFIDENTIALITY NOTICE: This email communication may contain private,
confidential, or legally privileged information intended for the sole
use of the designated and/or duly authorized recipient(s). If you are
not the intended recipient or have received this email in error, please
notify the sender immediately by email and permanently delete all copies
of this email including all attachments without reading them. If you are
the intended recipient, secure the contents in a manner that conforms to
all applicable state and/or federal requirements related to privacy and
confidentiality of such information.

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End of galaxy-user Digest, Vol 57, Issue 26
*******************************************

___________________________________________________________
The Galaxy User list should be used for the discussion of
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at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
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   http://lists.bx.psu.edu/


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
___________________________________________________________
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
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