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

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