There seems to be no description of how to run tophat if you are using unpaired sequence reads. Does it only work for mated pairs?
When I give it my commands, this is the error:
Error: you must set the mean inner distance between mates with -r
But, I don't have mates?
When I give it my commands, this is the error:
Error: you must set the mean inner distance between mates with -r
But, I don't have mates?
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