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 Seggewiß 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
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/
--
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.
attachment: golharam.vcf___
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/
