Hi,
Does anyone know why CuffDiff (part of the CuffLinks suite) accepts parameters for the expected distance between paired end reads, and also for the number of threads to be used for alignment e.g.
--inner-dist-mean
--inner-dist-std-dev
--num-threads
I was under the impression that CuffDiff doesn't do any alignment, and would have no use for these parameters?
Thanks.
Does anyone know why CuffDiff (part of the CuffLinks suite) accepts parameters for the expected distance between paired end reads, and also for the number of threads to be used for alignment e.g.
--inner-dist-mean
--inner-dist-std-dev
--num-threads
I was under the impression that CuffDiff doesn't do any alignment, and would have no use for these parameters?
Thanks.
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