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Question: Galaxy Bowtie Alignment Stats Report
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gravatar for Eric Guo
7.0 years ago by
Eric Guo • 60
Eric Guo • 60 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
alignment bowtie • 1.5k views
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modified 6.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.0 years ago by Eric Guo • 60
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gravatar for Jennifer Hillman Jackson
6.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENT • link written 6.9 years ago by Jennifer Hillman Jackson ♦ 25k
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