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Old 03-29-2011, 10:49 AM   #1
unidodo
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Default Bowtie ouput in Tophat

Just wondering if anyone knows how to get Bowtie output such as % of mapped unique reads when we run Tophat?

Thanks in advance.
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Old 03-29-2011, 12:22 PM   #2
ttnguyen
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I don't think we can get Bowtie mapping summary if we use Tophat since Tophat may split your reads and employes Bowtie at several steps. I think you might find that information by looking at accepted_hits.bam
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Old 03-30-2011, 01:13 PM   #3
unidodo
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Finally, I found such info in the files under the tophat output folder.

There are two files. One is the genome, another is the junction sequences.

Last edited by unidodo; 03-30-2011 at 01:24 PM.
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