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Just wondering if anyone knows how to get Bowtie output such as % of mapped unique reads when we run Tophat?
Thanks in advance.
Thanks in advance.
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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 -
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, 12:24 PM.Comment
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