Hello Eric, There are a few choices: flagstat BAM Index Statistics SAM/BAM Alignment Summary Metrics Use "Options -> Show Tool Search" and enter the tool name (in the left tool panel) to locate these and other tools quickly. Best, Jen Galaxy team On 12/8/11 4:02 PM, Eric Guo wrote:

Hello,

Does anyone know how to get alignment stats from Bowtie on Galaxy? I would like to know what percentage of total reads from my dataset is aligned.

I know if you run Bowtie using the command line, it gives you the report. However, I could not find percent alignment on Galaxy.

Thanks in advance for the help!

-Eric

___________________________________________________________ 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/wiki/Support