Hello Irene,
Both can be used with a custom reference genome - there is no difference
between the tools in that regard. However, Bowtie is for mapping DNA and
Tophat is for mapping RNA. More details are on the tool forms, including
links to the primary tool home pages.
Hopefully this helps,
Jen
Galaxy team
On 8/11/12 10:09 AM, i b wrote:
Hi all,
what is the difference between using "NGS:mapping-------Map with
Bowtie for Illumina" and "NGS: RNA analysis---------Tophat for
Illumina" when mapping reads against a reference/custom genome?
thanks,
ib
___________________________________________________________
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://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
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/