Using the tophat/cufflinks combo to find differential alternative splicing.
The cuffdiff manual says that if there "not enough alignments for testing" then you will get NOTEST and the treatments will not be compared. Does anyone have an idea as to what the cutoff for this is? Many of the genes that get NOTEST in my data set (single end) have a large number of reads (several hundred). Could it be because of insufficient coverage? or maybe operator error?
thanks!
The cuffdiff manual says that if there "not enough alignments for testing" then you will get NOTEST and the treatments will not be compared. Does anyone have an idea as to what the cutoff for this is? Many of the genes that get NOTEST in my data set (single end) have a large number of reads (several hundred). Could it be because of insufficient coverage? or maybe operator error?
thanks!
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