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TopHat coverage-search vs no-coverage-search option
So I am working on TopHat with RNA-Seq paired end illumina reads 100bp long, and the runtime is huge to say the least!!! the read files are 3.1gigs in size which means a total of 6gb worth of reads.
So my question is this, is all that runtime really worth it?
taking into consideration that I really am trying to predict novel transcripts will i be sacrificing a lot if i turn off coverage?
Can anyone shed some light on this because i am sure someone must have some experience with the question i am asking.
So my question is this, is all that runtime really worth it?
taking into consideration that I really am trying to predict novel transcripts will i be sacrificing a lot if i turn off coverage?
Can anyone shed some light on this because i am sure someone must have some experience with the question i am asking.