I was amazed to see that just last month @GTExPortal published its main paper with TopHat 1.4 https://www.nature.com/nature/journal/v550/n7675/full/nature24277.html … That's not even the most recent version of TopHat! There have been 16 releases since then (2012), the most recent in 2016. And that's 3 *programs* ago!
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Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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I've seen this plea to stop using Tophat before, and I've even seen reviewers knock proposals for using it. But while there may be no reason to use it, it would be useful to list the reasons to NOT use it other than age. 1/
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The reason not to use it is performance. "TopHat2 is consistently among the worst performers on both human and malaria T2 and T3 libraries." https://www.nature.com/articles/nmeth.4106 … There are many other published benchmarks corroborating this result.
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Just remove releases from the tophat website!
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It's not my website. cc
@StevenSalzberg1.
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I rt'd this but a colleague suggested I reply in this thread: to be accurate, TopHat was developed by Cole Trapnell (1st), Lior, and me. (I shouldn't have to explain this but....) TopHat2's primary developer was Daehwan Kim
@infphilo, who also built HISAT.Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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My guess is that a lot of people like your nature protocol paper that easily lays out RNA-seq analysis steps. Maybe writing a new protocol paper might get the change you seek
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My GATK protocol paper from 2013 gets tons of citations despite being horribly out of date. Though I'm not convinced it's what people are doing in practice; it might be just what they're citing because we don't have more appropriate citable papers. We're working on fixing that.
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Possibly folk using TopHat2 and citing the wrong paper but still...
Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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We are also seeing some people still using TopHat in Sweden... It was a big hit and now it is hard to fight with old habits, set-up pipelines and lag in publications. We are with you,
#methodsmatter and there should be no excuses here anymore. We do our best to stop the trend!Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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