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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Jennifer Jackson
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___________________________________________________________
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:
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
