User: Kevin Silverstein

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Posts by Kevin Silverstein

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Suggestion To Change Cuffdiff -C "Min Alignment Count" Default To Author'S Value Of '10'
... Hi Galaxy Developers, This is regarding the wrapper for cuffdiff and the -c parameter for "Min alignment count". We noted that Galaxy's default value is set to 1000. In our experience, setting this parameter that high yields drastically different results from the ones obtained with the author's ...
galaxy written 5.6 years ago by Kevin Silverstein20 • updated 5.6 years ago by Jeremy Goecks2.2k
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Answer: A: About Mapping Quality
... Jeremy, This is not strictly correct. Tophat/bowtie don't report mapping quality values that are as meaningful as BWA, but there is some information in the mapping quality values tophat reports. Tophat yields 4 distinct values for its mapping quality values (you can do a "unique" count on the ma ...
written 5.8 years ago by Kevin Silverstein20

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