Hello Shalabh,

BWA is a good choice for longer reads, if they are DNA. If you have RNA data, then you might want to consider a tool like BLAT or BLAST (is wrapped for Galaxy in the Tool Shed).


To use BLAST in Galaxy, you will need a local or cloud instance, as explained here:
http://getgalaxy.org
http://galaxyproject.org/wiki/Tool%20Shed

Hopefully this helps,

Jen
Galaxy team

On 10/3/11 7:50 AM, Shalabh Sharma wrote:
Hi,
I am new to mapping.
I have reads ranging from 150-300bp, i am not sure which is the best
suitable program for that in Galaxy.
I already tried bwa but i am not sure if thats the best choice for long
reads.

Thanks
Shalabh



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