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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