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Old 12-12-2012, 08:04 AM   #1
all_your_base
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Location: USA

Join Date: Mar 2012
Posts: 40
Default Determining alignment rate for Tophat

Hi,

I was just wondering if anyone could tell me the best way to find the overall alignment rate for a tophat run. I like how Bowtie outputs the alignment stats with an overall alignment rate as stdout, and am looking for something similar for Tophat.

I found that in the tophat_out/logs folder I can find the overall alignment rate for the left and right reads separately. Can I just average these to find the overall alignment rate?

Thanks for any suggestions.
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